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05 isescan plasmidfinder export pip -i参数 singularity使用安装metawrap phyloflash安装apptainer

作者：IT小白 | 2024-07-11 02:05:26

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plasmidfinder

Manual install (install from source code)

  • Install ISEScan

    • Download the latest ISEScan from https://github.com/xiezhq/ISEScan/releases, e.g. Source code (tar.gz).

    • Uncompress the .zip (or .tar.gz) file.

      • Use unzip command to uncompress the zip file:
       unzip v1.7.2.2.zip
      • Use tar command to uncompress the tar.gz file:
       tar -zvxf v1.7.2.2.tar.gz

      This will create a ISEScan folder, e.g. ISEScan-1.7.2.2. You need to go to ISEScan folder to configure and run it.

       cd ISEScan-1.7.2.2

  • Install dependencies before you run ISEScan

    • Python 3.3.3 or later     可以使用conda安装 挺快
    • numpy-1.8.0 or later  这一步不用安装 因为在安装fastcluster时候会自动安装
    • scipy-0.13.1 or later   使用pipin stall   -i  https://pypi.douban.com/simple/安装
    • fastcluster, latest version recommended, fastcluster · PyPI
    • FragGeneScan1.30 or earlier, (The .faa file output by version1.31 is not compatible with ISEScan!), FragGeneScan
    • HMMER-3.1b2 or later,       HMMER3.1使用 - 简书    HMMER conda安装hen's   HMMER
    • BLAST 2.2.31 or later
    • SSW Library, the latest version is not tested with ISEScan and the tested version of SSW library is shipped with ISEScan, please find it at ssw201507 subdirectory.
      • To use the shipped SSW library in ISEScan, please go to ssw201507 and then compile the codes by gcc:
      1.  cd ssw201507
      2.  gcc -Wall -O3 -pipe -fPIC -shared -rdynamic -o libssw.so ssw.c ssw.h
      • And then copy libssw.so and set search path:
      1.  cp libssw.so ../
      2.  export LD_LIBRARY_PATH=/home/xiezhq/projects/ISEScan-1.7.2.2:$LD_LIBRARY_PATH
      In command export LD_LIBRARY_PATH=/home/xiezhq/projects/ISEScan-1.7.2.2:$LD_LIBRARY_PATH, please replace /home/xiezhq/projects/ISEScan-1.7.2.2 with the actual path of libssw.so on your computer!
    • biopython 1.62 or later (required by SSW library)

  • Add the required packages to your $PATH before you run ISEScan

    • Add to $PATH the paths pointing to run_FragGeneScan.pl, phmmer, hmmsearch, blastn, blastp, makeblastdb
     export PATH=$PATH:/apps/inst/FragGeneScan1.30:/apps/inst/hmmer-3.3/bin:/apps/inst/ncbi-blast-2.10.0+/bin

    In command export above, please replace /apps/inst/FragGeneScan1.30, /apps/inst/hmmer-3.3/bin and /apps/inst/ncbi-blast-2.10.0+/bin with the actual paths of FragGeneScan, HMMER and BLAST on your computer!

kobas

  1. conda create -n kobas python=2.7
  2. #使用activate激活环境直接安装
  3. conda activate kobas
  4. conda install -c bioconda  kobas==3.0.3

metagenemark

MetaGeneMark-2-exp/reproduce.pdf at master · gatech-genemark/MetaGeneMark-2-exp · GitHub

$ conda install -c bioconda metaphlan

mgrast

GitHub - MG-RAST/MG-RAST-Tools: Repository of script tools, examples, and contributed code for using the MG-RAST API

GitHub - MG-RAST/MG-RAST-Tools: Repository of script tools, examples, and contributed code for using the MG-RAST API

motusGitHub - HRGV/phyloFlash: phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.

nt nr 

NR/NT，Taxonomy和RefSeq——三种NCBI常见数据库 - 大漠胡天 - 博客园 (cnblogs.com)

cd ${db}
    mkdir -p NCBI_nt && cd NCBI_nt
    wget -c "ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt.*.tar.gz" 

mkdir -p NCBI_nr && cd NCBI_nr

phyloflash 从头安装

YAMDA/README.md at master · daquang/YAMDA · GitHub

conda install -c bioconda pybedtools

phyloFlash | phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore the phylogenetic composition of an Illumina (meta)genomic dataset.

https://github.com/daquang/YAMDA/blob/master/README.md

bioinformatics-cafe/fastaFromBed at master · dariober/bioinformatics-cafe · GitHub

3、添入环境变量

echo 'export PATH=~/.aspera/connect/bin/:$PATH' >> ~/.bashrc
source ~/.bashrc

plasflow 自建频道 自建channel

https://github.com/smaegol/PlasFlow

 smaegol :: Anaconda.org

qiime2

Conda安装qiime2（目前最有效的方法） - 简书

QIIME 2 command-line interface (q2cli) — QIIME 2 2022.11.1 documentation

QIIME 2

Installing QIIME 2 — QIIME 2 2022.11.1 documentation

signalp5 signalp6

Signalp6 :: Anaconda.org

Services- DTU Health Tech

 Signalp5 :: Anaconda.org

GitHub - chenxi-zhang-art/signalP

tar -xzvf signalp-5.0b.Linux.tar.gz 
https://github.com/fteufel/signalp-6.0/blob/main/installation_instructions.md

  1. Description
  2. A placeholder package for SignalP v5.
  3.  
  4. Due to license restrictions, this recipe cannot distribute signalp5 directly. Please download signalp-5.0b.Linux.tar.gz from: https://services.healthtech.dtu.dk/services/SignalP-5.0b/9-Downloads.php#
  5.  
  6. and run the following command to complete the installation:
  7.  
  8. $ signalp5-register signalp-5.0b.Linux.tar.gz
  9. This will copy signalp5 into your conda environment.

pip install signalp-6-package/ -i  https://pypi.douban.com/
simple/

plasmidfinder

https://github.com/kcri-tz/plasmidfinder

魔鬼报错

  1. conda install -c bioconda -c conda-for
  2. ge plasmidfinderCollecting package metadata (current_repodata.json): done
  3. Solving environment: done
  4.  
  5. ## Package Plan ##
  6.  
  7.   environment location: /share/app/miniconda3/envs/plasmidfinder
  8.  
  9.   added / updated specs:
  10.     - plasmidfinder
  11.  
  12.  
  13. The following packages will be downloaded:
  14.  
  15.     package                    |            build
  16.     ---------------------------|-----------------
  17.     biopython-1.80             |  py311hd4cff14_0         2.9 MB  conda-forge
  18.     boost-1.80.0               |  py311h59ea3da_4         358 KB  conda-forge
  19.     boost-cpp-1.80.0           |       h75c5d50_0        17.4 MB  conda-forge
  20.     cgecore-1.5.6              |     pyh3252c3a_0          34 KB  bioconda
  21.     kma-1.4.9                  |       h7132678_0         261 KB  bioconda
  22.     numpy-1.24.2               |  py311h8e6699e_0         7.4 MB  conda-forge
  23.     plasmidfinder-2.1.6        |  py310hdfd78af_1         1.7 MB  bioconda
  24.     tabulate-0.9.0             |     pyhd8ed1ab_1          35 KB  conda-forge
  25.     ------------------------------------------------------------
  26.                                            Total:        30.1 MB
  27.  
  28. The following NEW packages will be INSTALLED:
  29.  
  30.   _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge 
  31.   _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-2_gnu 
  32.   biopython          conda-forge/linux-64::biopython-1.80-py311hd4cff14_0 
  33.   blast              bioconda/linux-64::blast-2.5.0-hc0b0e79_3 
  34.   boost              conda-forge/linux-64::boost-1.80.0-py311h59ea3da_4 
  35.   boost-cpp          conda-forge/linux-64::boost-cpp-1.80.0-h75c5d50_0 
  36.   bzip2              conda-forge/linux-64::bzip2-1.0.8-h7f98852_4 
  37.   ca-certificates    conda-forge/linux-64::ca-certificates-2022.12.7-ha878542_0 
  38.   cgecore            bioconda/noarch::cgecore-1.5.6-pyh3252c3a_0 
  39.   icu                conda-forge/linux-64::icu-70.1-h27087fc_0 
  40.   kma                bioconda/linux-64::kma-1.4.9-h7132678_0 
  41.   ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.40-h41732ed_0 
  42.   libblas            conda-forge/linux-64::libblas-3.9.0-16_linux64_openblas 
  43.   libcblas           conda-forge/linux-64::libcblas-3.9.0-16_linux64_openblas 
  44.   libffi             conda-forge/linux-64::libffi-3.4.2-h7f98852_5 
  45.   libgcc-ng          conda-forge/linux-64::libgcc-ng-12.2.0-h65d4601_19 
  46.   libgfortran-ng     conda-forge/linux-64::libgfortran-ng-12.2.0-h69a702a_19 
  47.   libgfortran5       conda-forge/linux-64::libgfortran5-12.2.0-h337968e_19 
  48.   libgomp            conda-forge/linux-64::libgomp-12.2.0-h65d4601_19 
  49.   liblapack          conda-forge/linux-64::liblapack-3.9.0-16_linux64_openblas 
  50.   libnsl             conda-forge/linux-64::libnsl-2.0.0-h7f98852_0 
  51.   libopenblas        conda-forge/linux-64::libopenblas-0.3.21-pthreads_h78a6416_3 
  52.   libsqlite          conda-forge/linux-64::libsqlite-3.40.0-h753d276_0 
  53.   libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-12.2.0-h46fd767_19 
  54.   libuuid            conda-forge/linux-64::libuuid-2.32.1-h7f98852_1000 
  55.   libzlib            conda-forge/linux-64::libzlib-1.2.13-h166bdaf_4 
  56.   ncurses            conda-forge/linux-64::ncurses-6.3-h27087fc_1 
  57.   numpy              conda-forge/linux-64::numpy-1.24.2-py311h8e6699e_0 
  58.   openssl            conda-forge/linux-64::openssl-3.0.7-h0b41bf4_2 
  59.   pip                conda-forge/noarch::pip-23.0-pyhd8ed1ab_0 
  60.   plasmidfinder      bioconda/noarch::plasmidfinder-2.1.6-py310hdfd78af_1 
  61.   python             conda-forge/linux-64::python-3.11.0-he550d4f_1_cpython 
  62.   python_abi         conda-forge/linux-64::python_abi-3.11-3_cp311 
  63.   readline           conda-forge/linux-64::readline-8.1.2-h0f457ee_0 
  64.   setuptools         conda-forge/noarch::setuptools-67.1.0-pyhd8ed1ab_0 
  65.   tabulate           conda-forge/noarch::tabulate-0.9.0-pyhd8ed1ab_1 
  66.   tk                 conda-forge/linux-64::tk-8.6.12-h27826a3_0 
  67.   tzdata             conda-forge/noarch::tzdata-2022g-h191b570_0 
  68.   wheel              conda-forge/noarch::wheel-0.38.4-pyhd8ed1ab_0 
  69.   xz                 conda-forge/linux-64::xz-5.2.6-h166bdaf_0 
  70.   zlib               conda-forge/linux-64::zlib-1.2.13-h166bdaf_4 
  71.   zstd               conda-forge/linux-64::zstd-1.5.2-h3eb15da_6 
  72.  
  73.  
  74. Proceed ([y]/n)? y
  75.  
  76.  
  77. Downloading and Extracting Packages
  78.                                                                                                           
  79.                                                                                                           
  80. CondaError: Downloaded bytes did not match Content-Length                                                 
  81.   url: https://conda.anaconda.org/conda-forge/linux-64/numpy-1.24.2-py311h8e6699e_0.conda                 
  82.   target_path: /share/app/miniconda3/pkgs/numpy-1.24.2-py311h8e6699e_0.conda                              
  83.   Content-Length: 7720502                                                                                 
  84.   downloaded bytes: 6650303                                                                               
  85.                                                                                                           
  86. CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://conda.anaconda.org/conda-forge/linux-64/boost-
  87. cpp-1.80.0-h75c5d50_0.tar.bz2>Elapsed: -
  88.  
  89. An HTTP error occurred when trying to retrieve this URL.
  90. HTTP errors are often intermittent, and a simple retry will get you on your way.
  91.  
  92.  
  93. (plasmidfinder) root@mgt:/share/app/miniconda3/envs/arg/conda-meta# conda install -c bioconda -c conda-for
  94. ge plasmidfinderCollecting package metadata (current_repodata.json): failed
  95.  
  96. # >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
  97.  
  98.     Traceback (most recent call last):
  99.       File "/share/app/miniconda3/lib/python3.10/site-packages/urllib3/response.py", line 761, in _update_
  100. chunk_length        self.chunk_left = int(line, 16)
  101.     ValueError: invalid literal for int() with base 16: b''
  102.     
  103.     During handling of the above exception, another exception occurred:
  104.     
  105.     Traceback (most recent call last):
  106.       File "/share/app/miniconda3/lib/python3.10/site-packages/urllib3/response.py", line 444, in _error_c
  107. atcher        yield
  108.       File "/share/app/miniconda3/lib/python3.10/site-packages/urllib3/response.py", line 828, in read_chu
  109. nked        self._update_chunk_length()
  110.       File "/share/app/miniconda3/lib/python3.10/site-packages/urllib3/response.py", line 765, in _update_
  111. chunk_length        raise InvalidChunkLength(self, line)
  112.     urllib3.exceptions.InvalidChunkLength: InvalidChunkLength(got length b'', 0 bytes read)
  113.     
  114.     During handling of the above exception, another exception occurred:
  115.     
  116.     Traceback (most recent call last):
  117.       File "/share/app/miniconda3/lib/python3.10/site-packages/requests/models.py", line 816, in generate
  118.         yield from self.raw.stream(chunk_size, decode_content=True)
  119.       File "/share/app/miniconda3/lib/python3.10/site-packages/urllib3/response.py", line 624, in stream
  120.         for line in self.read_chunked(amt, decode_content=decode_content):
  121.       File "/share/app/miniconda3/lib/python3.10/site-packages/urllib3/response.py", line 816, in read_chu
  122. nked        with self._error_catcher():
  123.       File "/share/app/miniconda3/lib/python3.10/contextlib.py", line 153, in __exit__
  124.         self.gen.throw(typ, value, traceback)
  125.       File "/share/app/miniconda3/lib/python3.10/site-packages/urllib3/response.py", line 461, in _error_c
  126. atcher        raise ProtocolError("Connection broken: %r" % e, e)
  127.     urllib3.exceptions.ProtocolError: ("Connection broken: InvalidChunkLength(got length b'', 0 bytes read
  128. )", InvalidChunkLength(got length b'', 0 bytes read))    
  129.     During handling of the above exception, another exception occurred:
  130.     
  131.     Traceback (most recent call last):
  132.       File "/share/app/miniconda3/lib/python3.10/site-packages/conda/exceptions.py", line 1118, in __call_
  133. _        return func(*args, **kwargs)
  134.       File "/share/app/miniconda3/lib/python3.10/site-packages/conda/cli/main.py", line 69, in main_subshe
  135. ll        exit_code = do_call(args, p)
  136.       File "/share/app/miniconda3/lib/python3.10/site-packages/conda/cli/conda_argparse.py", line 91, in d
  137. o_call        return getattr(module, func_name)(args, parser)
  138.       File "/share/app/miniconda3/lib/python3.10/site-packages/conda/notices/core.py", line 109, in wrappe
  139. r        return func(*args, **kwargs)
  140.       File "/share/app/miniconda3/lib/python3.10/site-packages/conda/cli/main_install.py", line 20, in exe
  141. cute        install(args, parser, 'install')
  142.       File "/share/app/miniconda3/lib/python3.10/site-packages/conda/cli/install.py", line 264, in install
  143.         unlink_link_transaction = solver.solve_for_transaction(
  144.       File "/share/app/miniconda3/lib/python3.10/site-packages/conda/core/solve.py", line 136, in solve_fo
  145. r_transaction        unlink_precs, link_precs = self.solve_for_diff(update_modifier, deps_modifier,
  146.       File "/share/app/miniconda3/lib/python3.10/site-packages/conda/core/solve.py", line 179, in solve_fo
  147. r_diff        final_precs = self.solve_final_state(update_modifier, deps_modifier, prune, ignore_pinned,
  148.       File "/share/app/miniconda3/lib/python3.10/site-packages/conda/core/solve.py", line 284, in solve_fi
  149. nal_state        ssc = self._collect_all_metadata(ssc)
  150.       File "/share/app/miniconda3/lib/python3.10/site-packages/conda/common/io.py", line 84, in decorated
  151.         return f(*args, **kwds)
  152.       File "/share/app/miniconda3/lib/python3.10/site-packages/conda/core/solve.py", line 451, in _collect
  153. _all_metadata        index, r = self._prepare(prepared_specs)
  154.       File "/share/app/miniconda3/lib/python3.10/site-packages/conda/core/solve.py", line 1061, in _prepar
  155. e        reduced_index = get_reduced_index(self.prefix, self.channels,
  156.       File "/share/app/miniconda3/lib/python3.10/site-packages/conda/core/index.py", line 272, in get_redu
  157. ced_index        new_records = SubdirData.query_all(spec, channels=channels, subdirs=subdirs,
  158.       File "/share/app/miniconda3/lib/python3.10/site-packages/conda/core/subdir_data.py", line 142, in qu
  159. ery_all        result = tuple(concat(executor.map(subdir_query, channel_urls)))
  160.       File "/share/app/miniconda3/lib/python3.10/concurrent/futures/_base.py", line 621, in result_iterato
  161. r        yield _result_or_cancel(fs.pop())
  162.       File "/share/app/miniconda3/lib/python3.10/concurrent/futures/_base.py", line 319, in _result_or_can
  163. cel        return fut.result(timeout)
  164.       File "/share/app/miniconda3/lib/python3.10/concurrent/futures/_base.py", line 458, in result
  165.         return self.__get_result()
  166.       File "/share/app/miniconda3/lib/python3.10/concurrent/futures/_base.py", line 403, in __get_result
  167.         raise self._exception
  168.       File "/share/app/miniconda3/lib/python3.10/concurrent/futures/thread.py", line 58, in run
  169.         result = self.fn(*self.args, **self.kwargs)
  170.       File "/share/app/miniconda3/lib/python3.10/site-packages/conda/core/subdir_data.py", line 131, in <l
  171. ambda>        subdir_query = lambda url: tuple(
  172.       File "/share/app/miniconda3/lib/python3.10/site-packages/conda/core/subdir_data.py", line 147, in qu
  173. ery        self.load()
  174.       File "/share/app/miniconda3/lib/python3.10/site-packages/conda/core/subdir_data.py", line 213, in lo
  175. ad        _internal_state = self._load()
  176.       File "/share/app/miniconda3/lib/python3.10/site-packages/conda/core/subdir_data.py", line 303, in _l
  177. oad        raw_repodata_str = fetch_repodata_remote_request(
  178.       File "/share/app/miniconda3/lib/python3.10/site-packages/conda/core/subdir_data.py", line 571, in fe
  179. tch_repodata_remote_request        resp = session.get(
  180.       File "/share/app/miniconda3/lib/python3.10/site-packages/requests/sessions.py", line 600, in get
  181.         return self.request("GET", url, **kwargs)
  182.       File "/share/app/miniconda3/lib/python3.10/site-packages/requests/sessions.py", line 587, in request
  183.         resp = self.send(prep, **send_kwargs)
  184.       File "/share/app/miniconda3/lib/python3.10/site-packages/requests/sessions.py", line 745, in send
  185.         r.content
  186.       File "/share/app/miniconda3/lib/python3.10/site-packages/requests/models.py", line 899, in content
  187.         self._content = b"".join(self.iter_content(CONTENT_CHUNK_SIZE)) or b""
  188.       File "/share/app/miniconda3/lib/python3.10/site-packages/requests/models.py", line 818, in generate
  189.         raise ChunkedEncodingError(e)
  190.     requests.exceptions.ChunkedEncodingError: ("Connection broken: InvalidChunkLength(got length b'', 0 by
  191. tes read)", InvalidChunkLength(got length b'', 0 bytes read))
  192. `$ /share/app/miniconda3/bin/conda install -c bioconda -c conda-forge plasmidfinder`
  193.  
  194.   environment variables:
  195.                  CIO_TEST=<not set>
  196.         CONDA_DEFAULT_ENV=plasmidfinder
  197.                 CONDA_EXE=/share/app/miniconda3/bin/conda
  198.              CONDA_PREFIX=/share/app/miniconda3/envs/plasmidfinder
  199.            CONDA_PREFIX_1=/share/app/miniconda3
  200.            CONDA_PREFIX_2=/share/app/miniconda3/envs/motus
  201.            CONDA_PREFIX_3=/share/app/miniconda3/envs/phyloflash
  202.            CONDA_PREFIX_4=/share/app/miniconda3
  203.            CONDA_PREFIX_5=/share/app/miniconda3/envs/plasflow
  204.     CONDA_PROMPT_MODIFIER=(plasmidfinder)
  205.          CONDA_PYTHON_EXE=/share/app/miniconda3/bin/python
  206.                CONDA_ROOT=/share/app/miniconda3
  207.               CONDA_SHLVL=6
  208.            CURL_CA_BUNDLE=<not set>
  209.      JAVA_LD_LIBRARY_PATH=:-:-:-:-:-:-:-
  210.           LD_LIBRARY_PATH=/public/arg/ISEScan-1.7.2.3:/public/arg/ISEScan-1.7.2.3:
  211.                LD_PRELOAD=<not set>
  212.                   MANPATH=/opt/xcat/share/man::/usr/bin/ypuser/man
  213.                MODULEPATH=/share/modulefiles:/root/modulefiles:/usr/share/Modules/modulefiles:/s
  214.                           hare/app/oneapi2022/modulefiles
  215.                      PATH=/public/arg/phyloFlash-
  216.                           pf3.4:/public/arg/FragGeneScan:/public/nanoplot/ncbi-blast-
  217.                           2.13.0+/bin:/public/nanoplot/centrifuge-1.0.3-
  218.                           beta:/public/nanoplot/sratoolkit.2.10.8-
  219.                           centos_linux64/bin:/public/metagenome/microbiome_helper-master:/share/
  220.                           app/miniconda3/envs/plasmidfinder/bin:/public/arg/FragGeneScan:/public
  221.                           /nanoplot/ncbi-blast-2.13.0+/bin:/public/nanoplot/centrifuge-1.0.3-
  222.                           beta:/public/nanoplot/sratoolkit.2.10.8-
  223.                           centos_linux64/bin:/public/metagenome/microbiome_helper-master:/share/
  224.                           app/miniconda3/bin:/share/app/miniconda3/condabin:/share/app/miniconda
  225.                           3/bin:/opt/xcat/bin:/opt/xcat/sbin:/opt/xcat/share/xcat/tools:/usr/lib
  226.                           64/qt-
  227.                           3.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/bin/ypu
  228.                           ser:/root/bin
  229.        REQUESTS_CA_BUNDLE=<not set>
  230.             SSL_CERT_FILE=<not set>
  231.  
  232.      active environment : plasmidfinder
  233.     active env location : /share/app/miniconda3/envs/plasmidfinder
  234.             shell level : 6
  235.        user config file : /root/.condarc
  236.  populated config files : 
  237.           conda version : 22.11.1
  238.     conda-build version : not installed
  239.          python version : 3.10.9.final.0
  240.        virtual packages : __archspec=1=x86_64
  241.                           __glibc=2.17=0
  242.                           __linux=3.10.0=0
  243.                           __unix=0=0
  244.        base environment : /share/app/miniconda3  (writable)
  245.       conda av data dir : /share/app/miniconda3/etc/conda
  246.   conda av metadata url : None
  247.            channel URLs : https://conda.anaconda.org/bioconda/linux-64
  248.                           https://conda.anaconda.org/bioconda/noarch
  249.                           https://conda.anaconda.org/conda-forge/linux-64
  250.                           https://conda.anaconda.org/conda-forge/noarch
  251.                           https://repo.anaconda.com/pkgs/main/linux-64
  252.                           https://repo.anaconda.com/pkgs/main/noarch
  253.                           https://repo.anaconda.com/pkgs/r/linux-64
  254.                           https://repo.anaconda.com/pkgs/r/noarch
  255.           package cache : /share/app/miniconda3/pkgs
  256.                           /root/.conda/pkgs
  257.        envs directories : /share/app/miniconda3/envs
  258.                           /root/.conda/envs
  259.                platform : linux-64
  260.              user-agent : conda/22.11.1 requests/2.28.1 CPython/3.10.9 Linux/3.10.0-1160.el7.x86_64 centos
  261. /7.9.2009 glibc/2.17                UID:GID : 0:0
  262.              netrc file : None
  263.            offline mode : False
  264.  
  265.  
  266. An unexpected error has occurred. Conda has prepared the above report.
  267.  
  268. If submitted, this report will be used by core maintainers to improve
  269. future releases of conda.
  270. Would you like conda to send this report to the core maintainers? [y/N]: 
  271. Timeout reached. No report sent.

virsorter 

GitHub - jiarong/VirSorter2: customizable pipeline to identify viral sequences from (meta)genomic data

Virsorter :: Anaconda.org

  1. "Collecting package metadata (current_repodata.json): done" 表示 conda 正在收集当前存储库中的软件包元数据。元数据包括软件包的版本，依赖关系等信息，conda 需要这些信息来确定如何安装该软件包。
  2.  
  3. "Solving environment: failed with initial frozen solve. Retrying with flexible solve." 意味着 conda 在初始冻结的解决方案中失败了，因此在使用更加灵活的解决方案时再次尝试安装。这种情况通常表示与当前环境中的软件包冲突，导致 conda 无法安装 mamba。
  4.  
  5. 在这种情况下，建议您创建一个新的 conda 环境，并在该环境中安装该软件包，以避免与当前环境中的软件包冲突。您可以使用以下命令创建新环境：

Option 2 (development version)

The development version is most updated. To install the development version:

conda create -n vs2 -c conda-forge -c bioconda "python>=3.6" scikit-learn=0.22.1 imbalanced-learn pandas seaborn hmmer==3.3 prodigal screed ruamel.yaml "snakemake>=5.18,<=5.26" click mamba
conda activate vs2
git clone https://github.com/jiarong/VirSorter2.git
cd VirSorter2
pip install -e .

apptainer  singularity  centos系统

Getting Started | Apptainer

apptainer/INSTALL.md at main · apptainer/apptainer · GitHub

CentOS 7安装Development Tools失败 - 简书

sudo yum groupinstall -y 'Development Tools'
  1. On CentOS/RHEL:
  2.  
  3. # Install basic tools for compiling
  4. sudo yum groupinstall -y 'Development Tools'
  5. # Ensure EPEL repository is available
  6. sudo yum install -y epel-release
  7. # Install RPM packages for dependencies
  8. sudo yum install -y \
  9.     libseccomp-devel \
  10.     squashfs-tools \
  11.     squashfuse \
  12.     fuse-overlayfs \
  13.     fakeroot \
  14.     /usr/*bin/fuse2fs \
  15.     cryptsetup \
  16.     wget git

Downloads - The Go Programming Language

  1. udo tar -C /usr/local -xzf /tmp/go1.20.linux-amd64.tar.gz 什么意思
  2. The sudo tar -C /usr/local -xzf /tmp/go1.20.linux-amd64.tar.gz command has the following meaning:
  3.  
  4. sudo: The command is executed with superuser (root) privileges.
  5. tar: The tar (tape archive) command is used to extract files from a tar archive.
  6. -C /usr/local: The -C option specifies the directory (/usr/local) where the tar archive should be extracted.
  7. -xzf: The -x option extracts the files, the -z option uncompresses the archive using gzip, and the -f option specifies the archive file name (/tmp/go1.20.linux-amd64.tar.gz).
  8. So, the overall effect of the command is to extract the contents of the /tmp/go1.20.linux-amd64.tar.gz archive to the /usr/local directory.

 git clone --recursive https://github.com/apptainer/apptainer.git 需要加recursive比较稳妥

  1. Clone the repo
  2. With the adoption of Go modules you no longer need to clone the Apptainer repository to a specific location.
  3.  
  4. Clone the repository with git in a location of your choice:
  5.  
  6. git clone https://github.com/apptainer/apptainer.git
  7. cd apptainer
  8. By default your clone will be on the main branch which is where development of Apptainer happens. To build a specific version of Apptainer, check out a release tag before compiling, for example:
  9.  
  10. git checkout v1.1.5
  11. Compiling Apptainer
  12. You can configure, build, and install Apptainer using the following commands:
  13.  
  14. ./mconfig
  15. cd ./builddir
  16. make
  17. sudo make install

（Linux）make编译用法简述_漠效的博客-CSDN博客_make编译

make编译过程中用到的或者下载下来的文件在哪

  1. 【1】make
  2. 等同于 make all
  3.  
  4. 它是一个解释makefile中指令的命令工具
  5.  
  6. 执行make时，默认会去(当前文件夹下),找名为Makefile的文件
  7.  
  8. 根据Makefile文件来编译源代码，生成目标文件及可执行文件
  9.  
  10. 在每次使用make时,都会重新生成objects，新产生的object会覆盖旧的objects
  11.  
  12. 【2】make clean
  13. 清除以前的make命令编译后所产生的object文件(即后缀为“.o”的文件)及其生成的可执行文件
  14.  
  15. 一般来说，在每次使用make时,都会重新生成objects，新产生的object会覆盖旧的objects
  16.  
  17. 但是实际用时，经过多次编译后，必须使用make clean（直接make，以前留下来的错误不能清除干净）
  18.  
  19. 【3】make install
  20. 将编译成功的可执行文件移动到make编译时填写的目录，依据生成的makefile文件
  21.  
  22. 一般默认系统目录/usr/local/bin
  23.  
  24. 【4】make dist
  25. 产生发布软件包.
  26.  
  27. 即将可执行文件及相关文件打包成一个tar.gz格式的压缩文件，会在当前目录下生成XXX.tar.gz的文件
  28.  
  29. 【5】make distcheck
  30. 相当于make dist命令的进化版
  31.  
  32. 生成发布软件包并对其进行检查，以确定发布包的正确性
  33.  
  34. 它会自动把压缩包文件解开，然后执行configure命令，并且执行make，来确认编译不出现错误，并会在最后提示你软件包是否正确
  35.  
  36. 【6】make distclean
  37. 类似于make clean
  38.  
  39. 清除以前的make命令编译后所产生的object文件(即后缀为“.o”的文件)及其生成的可执行文件，并将configure生成的文件全部删除掉
  40.  
  41. 通常在使用make clean后使用，清理的更干净，避免影响再次编译
  42.  
  43. makefile概念
  44. makefile有些类似于脚本，通过定义了一系列的规则，指定哪些文件需要先编译，哪些文件需要后编译，哪些文件需要重新编译，甚至于进行更复杂的功能操作，并且它也可以执行操作系统的命令
  45.  
  46. 当编译安装源码包时，使用make编译，它会默认找当前目录下的makefile文件，依据makefile中的规则，执行编译安装
  47.  
  48. makefile可以实现自动化编译,原理上来说，只需要一个make命令，整个工程完全自动编译，极大的提高了软件开发的效率
  49.  
  50. makefile成为了一种被广泛应用于在工程方面的编译方法
  51. ————————————————
  52. 版权声明：本文为CSDN博主「漠效」的原创文章，遵循CC 4.0 BY-SA版权协议，转载请附上原文出处链接及本声明。
  53. 原文链接：https://blog.csdn.net/gx_1_11_real/article/details/81068412
  1. at Makefile 
  2. #
  3. # Non-recursive Makefile GENERATED by `mconfig' -- Wed Feb  8 02:10:40 CST 2023
  4. # configured: /public/arg/apptainer/mconfig --with-suid
  5. #
  7. # [ Embedding file : /public/arg/apptainer/builddir/makeit-intermediate/base.mk ] #
  9. # silent build
  10. V := @
  12. # source/build locations
  13. BUILDDIR := .
  14. BUILDDIR_ABSPATH := /public/arg/apptainer/builddir
  15. SOURCEDIR := /public/arg/apptainer
  16. SCRIPTSDIR := /public/arg/apptainer/mlocal/scripts
  17. CONTRIBDIR := 
  18. PREFIX := /usr/local
  19. EXECPREFIX := /usr/local
  20. BINDIR := /usr/local/bin
  21. SBINDIR := /usr/local/sbin
  22. LIBEXECDIR := /usr/local/libexec
  23. DATAROOTDIR := /usr/local/share
  24. DATADIR := /usr/local/share
  25. SYSCONFDIR := /usr/local/etc
  26. SHAREDSTATEDIR := /usr/local/com
  27. LOCALSTATEDIR := /usr/local/var
  28. RUNSTATEDIR := /usr/local/var/run
  29. INCLUDEDIR := /usr/local/include
  30. OLDINCLUDEDIR := /usr/include
  31. DOCDIR := /usr/local/share/doc/apptainer
  32. INFODIR := /usr/local/share/info
  33. HTMLDIR := /usr/local/share/doc/apptainer
  34. DVIDIR := /usr/local/share/doc/apptainer
  35. PDFDIR := /usr/local/share/doc/apptainer
  36. PSDIR := /usr/local/share/doc/apptainer
  37. LIBDIR := /usr/local/lib
  38. LOCALEDIR := /usr/local/share/locale
  39. MANDIR := /usr/local/share/man
  40. RPMPREFIX:=
  42. NAME := apptainer
  43. SHORT_VERSION := 1.1.5
  44. VERSION := 1.1.5
  46. HOSTAR := ar
  47. HOSTCC := cc
  48. HOSTCXX := c++
  49. HOSTLD := cc
  50. HOSTRANLIB := ranlib
  51. HOSTSIZE := size
  52. HOSTOBJCOPY := objcopy
  54. AR := ar
  55. CC := cc
  56. CXX := c++
  57. LD := ld
  58. RANLIB := ranlib
  59. SIZE := size
  60. OBJCOPY := objcopy
  62. ARCH := x86_64
  64. CFLAGS :=  -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -fstack-protector --param ssp-buffer-size=4 -Wal
  65. l -Werror -Wfatal-errors -Wno-unknown-warning-option -Wstrict-prototypes -Wpointer-arith -Wbad-function-cast -Woverlength-strings -Wframe-larger-than=2047 -Wno-sign-compare -Wclobbered -Wempty-body -Wmissing-parameter-type -Wtype-limits -Wunused-parameter -Wunused-but-set-parameter -Wno-discarded-qualifiers -Wno-incompatible-pointer-types -pipe -fmessage-length=0 -fPIC
  66. GO := /usr/local/go/bin/go
  68. CGO_CFLAGS := -I/public/arg/apptainer/builddir 
  69. CGO_LDFLAGS := 
  70. CGO_CPPFLAGS := 
  71. CGO_CXXFLAGS := 
  72. export CGO_CFLAGS CGO_LDFLAGS CGO_CPPFLAGS CGO_CXXFLAGS
  73. LDFLAGS := 
  75. # make sure `all' is the first rule
  76. all:
  78. # [ Embedding file :  /public/arg/apptainer/mlocal/frags/common_opts.mk ] #
  80. # a list of extra files to clean augmented by each module (*.mconf) file
  81. CLEANFILES :=
  83. # general build-wide compile options
  84. AFLAGS := -g
  86. LDFLAGS += -Wl,-z,relro,-z,now
  88. # [ Embedding file : /public/arg/apptainer/mlocal/frags/go_common_opts.mk ] #
  90. # go tool default build options
  91. GO111MODULE := on
  92. GO_TAGS := containers_image_openpgp sylog oci_engine apptainer_engine fakeroot_engine
  93. GO_TAGS_SUID := containers_image_openpgp sylog apptainer_engine fakeroot_engine
  94. GO_LDFLAGS :=
  95. # Need to use non-pie build on ppc64le
  96. # https://github.com/apptainer/singularity/issues/5762
  97. # Need to disable race detector on ppc64le
  98. # https://github.com/apptainer/singularity/issues/5914
  99. uname_m := $(shell uname -m)
  100. ifeq ($(uname_m),ppc64le)
  101. GO_BUILDMODE := -buildmode=default
  102. GO_RACE :=
  103. else
  104. GO_BUILDMODE := -buildmode=pie
  105. GO_RACE := -race
  106. endif
  107. GO_MODFLAGS := $(if $(wildcard $(SOURCEDIR)/vendor/modules.txt),-mod=vendor,-mod=readonly)
  108. GO_MODFILES := $(SOURCEDIR)/go.mod $(SOURCEDIR)/go.sum
  109. GOFLAGS := $(GO_MODFLAGS) -trimpath
  110. GOPROXY := https://proxy.golang.org
  112. export GOFLAGS GO111MODULE GOPROXY
  114. # [ Embedding file : /public/arg/apptainer/mlocal/frags/go_unix_opts.mk ] #
  116. GO_TAGS += apparmor selinux
  117. GO_TAGS_SUID += apparmor selinux
  119. # [ Embedding file : /public/arg/apptainer/mlocal/frags/go_runtime_opts.mk ] #
  121. CGO_CFLAGS += -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -fstack-protector --param ssp-buffer-size
  122. =4
  123. # [ Embedding file : /public/arg/apptainer/mlocal/frags/release_opts.mk ] #
  125. CFLAGS += -O2
  126. LDFLAGS += -s
  128. # [ Embedding file : /public/arg/apptainer/mlocal/frags/go_normal_opts.mk ] #
  130. # This tells go's link command to add a GNU Build Id, needed for later
  131. #   symbol stripping for example as is done by rpmbuild.
  132. GO_LDFLAGS += -ldflags="-B 0x`head -c20 /dev/urandom|od -An -tx1|tr -d ' \n'`"
  133.  
  134. # [ Embedding file : /public/arg/apptainer/mlocal/frags/arch_x86_64_opts.mk ] #
  135.  
  136.  
  137. # [ Embedding file : /public/arg/apptainer/builddir/makeit-intermediate/combined-mconfsready.mk ] #
  138.  
  139. # object files list
  140. _OBJ := \
  141.  
  142. # suffix rules (metarules missing from most variants)
  143.  
  144.  
  145. # [ Embedding file : /public/arg/apptainer/builddir/makeit-intermediate/all.mk ] #
  146.  
  147. all: $()
  148.  
  149. CLEANFILES += 
  150.  
  151. # [ Embedding file :    /public/arg/apptainer/mlocal/frags/build_cli.mk ] #
  152.  
  153. # This file contains all of the rules for building the apptainer CLI binary
  154.  
  155. # apptainer build config
  156. apptainer_build_config := $(SOURCEDIR)/internal/pkg/buildcfg/config.go
  157. $(apptainer_build_config): $(BUILDDIR)/config.h $(SOURCEDIR)/scripts/go-generate
  158. 	$(V)rm -f $(apptainer_build_config)
  159. 	$(V) cd $(SOURCEDIR)/internal/pkg/buildcfg && $(SOURCEDIR)/scripts/go-generate
  160.  
  161. CLEANFILES += $(apptainer_build_config)
  162.  
  163. # contain apptainer_SOURCE variable list
  164. apptainer_deps := $(BUILDDIR_ABSPATH)/apptainer.deps
  165.  
  166. -include $(apptainer_deps)
  167.  
  168. $(apptainer_deps): $(GO_MODFILES)
  169. 	@echo " GEN GO DEP" $@
  170. 	$(V)$(SOURCEDIR)/makeit/gengodep -v3 "$(GO)" "apptainer_SOURCE" "$(GO_TAGS)" "$@" "$(SOURCEDIR)/cmd
  171. /apptainer"
  172. # Look at dependencies file changes via apptainer_deps
  173. # because it means that a module was updated.
  174. apptainer := $(BUILDDIR)/apptainer
  175. $(apptainer): $(apptainer_build_config) $(apptainer_deps) $(apptainer_SOURCE)
  176. 	@echo " GO" $@; echo "    [+] GO_TAGS" \"$(GO_TAGS)\"
  177. 	$(V)$(GO) build $(GO_MODFLAGS) $(GO_BUILDMODE) -tags "$(GO_TAGS)" $(GO_LDFLAGS) \
  178. 		-o $(BUILDDIR)/apptainer $(SOURCEDIR)/cmd/apptainer
  180. apptainer_INSTALL := $(DESTDIR)$(BINDIR)/apptainer
  181. $(apptainer_INSTALL): $(apptainer)
  182. 	@echo " INSTALL" $@
  183. 	$(V)umask 0022 && mkdir -p $(@D)
  184. 	$(V)install -m 0755 $(apptainer) $(apptainer_INSTALL) # set cp to install
  186. singularity_INSTALL := $(DESTDIR)$(BINDIR)/singularity
  187. $(singularity_INSTALL):
  188. 	@echo " INSTALL" $@
  189. 	$(V)ln -sf apptainer $(singularity_INSTALL)
  191. CLEANFILES += $(apptainer)
  192. INSTALLFILES += $(apptainer_INSTALL) $(singularity_INSTALL)
  193. ALL += $(apptainer)
  196. # bash_completion files
  197. bash_completion1 :=  $(BUILDDIR)/etc/bash_completion.d/apptainer
  198. bash_completion2 :=  $(BUILDDIR)/etc/bash_completion.d/singularity
  199. bash_completions := $(bash_completion1) $(bash_completion2)
  200. $(bash_completions): $(apptainer_build_config)
  201. 	@echo " GEN" $@
  202. 	$(V)rm -f $@
  203. 	$(V)mkdir -p $(@D)
  204. 	$(V)$(GO) run $(GO_MODFLAGS) -tags "$(GO_TAGS)" \
  205. 		$(SOURCEDIR)/cmd/bash_completion/bash_completion.go $@
  207. bash_completion1_INSTALL := $(DESTDIR)$(DATADIR)/bash-completion/completions/apptainer
  208. bash_completion2_INSTALL := $(DESTDIR)$(DATADIR)/bash-completion/completions/singularity
  209. bash_completions_INSTALL := $(bash_completion1_INSTALL) $(bash_completion2_INSTALL)
  210. $(bash_completion1_INSTALL): $(bash_completion1)
  211. 	@echo " INSTALL" $@
  212. 	$(V)umask 0022 && mkdir -p $(@D)
  213. 	$(V)install -m 0644 $< $@
  215. $(bash_completion2_INSTALL): $(bash_completion2)
  216. 	@echo " INSTALL" $@
  217. 	$(V)umask 0022 && mkdir -p $(@D)
  218. 	$(V)install -m 0644 $< $@
  220. CLEANFILES += $(bash_completions)
  221. INSTALLFILES += $(bash_completions_INSTALL)
  222. ALL += $(bash_completions)
  225. # apptainer.conf file
  226. config := $(BUILDDIR)/apptainer.conf
  227. config_INSTALL := $(DESTDIR)$(SYSCONFDIR)/apptainer/apptainer.conf
  228. # override this to empty to avoid merging old configuration settings
  229. old_config := $(config_INSTALL)
  231. $(config): $(apptainer)
  232. 	@echo " GEN $@`if [ -n "$(old_config)" ]; then echo " from $(old_config)"; fi`"
  233. 	$(V)$(apptainer) confgen $(old_config) $(config)
  235. $(config_INSTALL): $(config)
  236. 	@echo " INSTALL" $@
  237. 	$(V)umask 0022 && mkdir -p $(@D)
  238. 	$(V)install -m 0644 $< $@
  240. INSTALLFILES += $(config_INSTALL)
  241. ALL += $(config)
  243. # remote config file
  244. remote_config := $(SOURCEDIR)/etc/remote.yaml
  246. remote_config_INSTALL := $(DESTDIR)$(SYSCONFDIR)/apptainer/remote.yaml
  247. $(remote_config_INSTALL): $(remote_config)
  248. 	@echo " INSTALL" $@
  249. 	$(V)umask 0022 && mkdir -p $(@D)
  250. 	$(V)install -m 0644 $< $@
  252. INSTALLFILES += $(remote_config_INSTALL)
  254. man_pages := $(BUILDDIR)$(MANDIR)/man1
  255. $(man_pages): apptainer
  256. 	@echo " MAN" $@
  257. 	mkdir -p $@
  258. 	$(V)$(GO) run $(GO_MODFLAGS) -tags "$(GO_TAGS)" \
  259. 		$(SOURCEDIR)/cmd/docs/docs.go man --dir $@
  260. 	$(V)cd $@;							\
  261. 		for M in apptainer*; do					\
  262. 			S="`echo $$M|sed 's/apptainer/singularity/'`";	\
  263. 			ln -fs $$M $$S;					\
  264. 		done
  266. man_pages_INSTALL := $(DESTDIR)$(MANDIR)/man1
  267. $(man_pages_INSTALL): $(man_pages)
  268. 	@echo " INSTALL" $@
  269. 	$(V)umask 0022 && mkdir -p $@
  270. 	$(V)install -m 0644 -t $@ $(man_pages)/*
  272. INSTALLFILES += $(man_pages_INSTALL)
  273. ALL += $(man_pages)
  275. # [ Embedding file : /public/arg/apptainer/mlocal/frags/build_network.mk ] #
  277. # This file contains rules for building CNI plugins which can enable
  278. #   different networking functions between container(s) and the host
  280. apptainer_REPO := github.com/apptainer/apptainer
  282. cni_builddir := $(BUILDDIR_ABSPATH)/cni
  283. cni_install_DIR := $(DESTDIR)$(LIBEXECDIR)/apptainer/cni
  284. cni_plugins := $(shell grep '^	_' $(SOURCEDIR)/internal/pkg/runtime/engine/apptainer/plugins_linux.go | c
  285. ut -d\" -f2)cni_plugins_EXECUTABLES := $(addprefix $(cni_builddir)/, $(notdir $(cni_plugins)))
  286. cni_plugins_INSTALL := $(addprefix $(cni_install_DIR)/, $(notdir $(cni_plugins)))
  287. cni_config_LIST := $(SOURCEDIR)/etc/network/00_bridge.conflist \
  288.                    $(SOURCEDIR)/etc/network/10_ptp.conflist \
  289.                    $(SOURCEDIR)/etc/network/20_ipvlan.conflist \
  290.                    $(SOURCEDIR)/etc/network/30_macvlan.conflist \
  291.                    $(SOURCEDIR)/etc/network/40_fakeroot.conflist
  292. cni_config_INSTALL := $(DESTDIR)$(SYSCONFDIR)/apptainer/network
  294. .PHONY: cniplugins
  295. cniplugins:
  296. 	$(V)umask 0022 && mkdir -p $(cni_builddir)
  297. 	$(V)for p in $(cni_plugins); do \
  298. 		name=`basename $$p`; \
  299. 		cniplugin=$(cni_builddir)/$$name; \
  300. 		if [ ! -f $$cniplugin ]; then \
  301. 			echo " CNI PLUGIN" $$name; \
  302. 		$(GO) build $(GO_MODFLAGS) $(GO_BUILDMODE) -tags "$(GO_TAGS)" $(GO_LDFLAGS) \
  303. 			-o $$cniplugin $$p; \
  304. 		fi \
  305. 	done

# run-singularity script
run_singularity := $(SOURCEDIR)/scripts/run-singularity

run_singularity_INSTALL := $(DESTDIR)$(BINDIR)/run-singularity
$(run_singularity_INSTALL): $(run_singularity)
    @echo " INSTALL" $@
    $(V)umask 0022 && mkdir -p $(@D)
    $(V)install -m 0755 $< $@

INSTALLFILES += $(run_singularity_INSTALL)


# capability config file
capability_config_INSTALL := $(DESTDIR)$(SYSCONFDIR)/apptainer/capability.json
$(capability_config_INSTALL):
    @echo " INSTALL" $@
    $(V)umask 0022 && mkdir -p $(@D)
    $(V)touch $@

INSTALLFILES += $(capability_config_INSTALL)

go env GOPATH 

make编译过程中用到的或者下载下来的文件在哪 go下载的临时文件都在哪里呢 通常在go env GOPATH 路径下面

  1.  ls -lha  /root/go/pkg/m
  2. od/cache/download/github.com/total 4.0K
  3. drwxr-xr-x 25 root root 4.0K Feb  8 02:14 .
  4. drwxr-xr-x  7 root root   91 Feb  8 02:13 ..
  5. drwxr-xr-x  3 root root   17 Feb  8 02:14 apex
  6. drwxr-xr-x  5 root root   77 Feb  8 02:13 apptainer
  7. drwxr-xr-x  3 root root   20 Feb  8 02:11 blang
  8. drwxr-xr-x  3 root root   24 Feb  8 02:13 containerd
  9. drwxr-xr-x  4 root root   32 Feb  8 02:11 containernetworking
  10. drwxr-xr-x  3 root root   19 Feb  8 02:11 containers
  11. drwxr-xr-x  3 root root   17 Feb  8 02:11 creack
  12. drwxr-xr-x  3 root root   33 Feb  8 02:13 cyphar
  13. drwxr-xr-x  4 root root   36 Feb  8 02:14 docker
  14. drwxr-xr-x  3 root root   19 Feb  8 02:13 fatih
  15. drwxr-xr-x  3 root root   17 Feb  8 02:14 go-log
  16. drwxr-xr-x  3 root root   18 Feb  8 02:11 google
  17. drwxr-xr-x  3 root root   18 Feb  8 02:14 gosimple
  18. drwxr-xr-x  3 root root   27 Feb  8 02:11 hashicorp
  19. drwxr-xr-x  8 root root  101 Feb  8 02:14 opencontainers
  20. drwxr-xr-x  3 root root   21 Feb  8 02:11 pelletier
  21. drwxr-xr-x  3 root root   20 Feb  8 02:11 pkg
  22. drwxr-xr-x  3 root root   23 Feb  8 02:11 !proton!mail
  23. drwxr-xr-x  3 root root   31 Feb  8 02:11 seccomp
  24. drwxr-xr-x  3 root root   21 Feb  8 02:13 shopspring
  25. drwxr-xr-x  4 root root   32 Feb  8 02:13 spf13
  26. drwxr-xr-x  3 root root   23 Feb  8 02:13 sylabs
  27. drwxr-xr-x  3 root root   17 Feb  8 02:13 vbauerster
  1. make
  2.  GO apptainer
  3.     [+] GO_TAGS "containers_image_openpgp sylog oci_engine apptainer_engine fakeroot_engine apparmor selin
  4. ux"go: downloading github.com/apptainer/container-key-client v0.8.0
  5. go: downloading github.com/apptainer/sif/v2 v2.8.1
  6. go: downloading github.com/fatih/color v1.13.0
  7. go: downloading golang.org/x/sys v0.0.0-20220715151400-c0bba94af5f8
  8. go: downloading github.com/apptainer/container-library-client v1.3.3
  9. go: downloading github.com/sylabs/json-resp v0.8.1
  10. go: downloading github.com/creack/pty v1.1.18
  11. go: downloading github.com/opencontainers/runtime-spec v1.0.3-0.20210326190908-1c3f411f0417
  12. go: downloading github.com/shopspring/decimal v1.3.1
  13. go: downloading github.com/ProtonMail/go-crypto v0.0.0-20220824120805-4b6e5c587895
  14. go: downloading gopkg.in/yaml.v2 v2.4.0
  15. go: downloading github.com/docker/go-units v0.4.0
  16. go: downloading golang.org/x/term v0.0.0-20210927222741-03fcf44c2211
  17. go: downloading github.com/spf13/cobra v1.5.0
  18. go: downloading github.com/containers/image/v5 v5.22.0
  19. go: downloading github.com/spf13/pflag v1.0.5
  20. go: downloading github.com/seccomp/containers-golang v0.6.0
  21. go: downloading github.com/containerd/containerd v1.6.8
  22. go: downloading github.com/blang/semver/v4 v4.0.0
  23. go: downloading github.com/pkg/errors v0.9.1
  24. go: downloading github.com/pelletier/go-toml v1.9.5
  25. go: downloading github.com/opencontainers/runc v1.1.4
  26. go: downloading github.com/opencontainers/go-digest v1.0.0
  27. go: downloading github.com/opencontainers/image-spec v1.0.2-0.20211117181255-693428a734f5
  28. go: downloading oras.land/oras-go v1.2.0
  29. go: downloading github.com/go-log/log v0.2.0
  30. go: downloading github.com/gosimple/slug v1.12.0
  31. go: downloading github.com/vbauerster/mpb/v7 v7.4.2
  32. go: downloading mvdan.cc/sh/v3 v3.5.1
  33. go: downloading github.com/cyphar/filepath-securejoin v0.2.3
  34. go: downloading github.com/google/uuid v1.3.0
  35. go: downloading github.com/apex/log v1.9.0
  36. go: downloading github.com/opencontainers/umoci v0.4.7
  37. go: downloading github.com/docker/docker v20.10.17+incompatible
  38. go: downloading github.com/opencontainers/selinux v1.10.1
  39. ../cmd/internal/cli/pgp.go:23:2: github.com/ProtonMail/go-crypto@v0.0.0-20220824120805-4b6e5c587895: Get "
  40. https://proxy.golang.org/github.com/%21proton%21mail/go-crypto/@v/v0.0.0-20220824120805-4b6e5c587895.zip": dial tcp 172.217.160.113:443: i/o timeout../pkg/sypgp/sypgp.go:35:2: github.com/ProtonMail/go-crypto@v0.0.0-20220824120805-4b6e5c587895: Get "https
  41. ://proxy.golang.org/github.com/%21proton%21mail/go-crypto/@v/v0.0.0-20220824120805-4b6e5c587895.zip": dial tcp 172.217.160.113:443: i/o timeout../cmd/internal/cli/pgp.go:24:2: github.com/ProtonMail/go-crypto@v0.0.0-20220824120805-4b6e5c587895: Get "
  42. https://proxy.golang.org/github.com/%21proton%21mail/go-crypto/@v/v0.0.0-20220824120805-4b6e5c587895.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/sources/oci_unpack.go:23:2: github.com/apex/log@v1.9.0: Get "https://proxy.golang.or
  43. g/github.com/apex/log/@v/v1.9.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/remote/endpoint/client.go:19:2: github.com/apptainer/container-key-client@v0.8.0: Get "htt
  44. ps://proxy.golang.org/github.com/apptainer/container-key-client/@v/v0.8.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/remote/endpoint/client.go:20:2: github.com/apptainer/container-library-client@v1.3.3: Get 
  45. "https://proxy.golang.org/github.com/apptainer/container-library-client/@v/v1.3.3.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/app/apptainer/sign.go:14:2: github.com/apptainer/sif/v2@v2.8.1: Get "https://proxy.golang.org/
  46. github.com/apptainer/sif/v2/@v/v2.8.1.zip": dial tcp 172.217.160.113:443: i/o timeout../pkg/image/sif.go:19:2: github.com/apptainer/sif/v2@v2.8.1: Get "https://proxy.golang.org/github.com/app
  47. tainer/sif/v2/@v/v2.8.1.zip": dial tcp 172.217.160.113:443: i/o timeout../cmd/internal/cli/siftool.go:15:2: github.com/apptainer/sif/v2@v2.8.1: Get "https://proxy.golang.org/git
  48. hub.com/apptainer/sif/v2/@v/v2.8.1.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/plugin/module.go:23:2: github.com/blang/semver/v4@v4.0.0: Get "https://proxy.golang.org/gi
  49. thub.com/blang/semver/v4/@v/v4.0.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/client/oras/oras.go:29:2: github.com/containerd/containerd@v1.6.8: Get "https://proxy.gola
  50. ng.org/github.com/containerd/containerd/@v/v1.6.8.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/client/oras/oras.go:30:2: github.com/containerd/containerd@v1.6.8: Get "https://proxy.gola
  51. ng.org/github.com/containerd/containerd/@v/v1.6.8.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/client/oras/oras.go:31:2: github.com/containerd/containerd@v1.6.8: Get "https://proxy.gola
  52. ng.org/github.com/containerd/containerd/@v/v1.6.8.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/client/oras/oras.go:32:2: github.com/containerd/containerd@v1.6.8: Get "https://proxy.gola
  53. ng.org/github.com/containerd/containerd/@v/v1.6.8.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/oci/oci.go:22:2: github.com/containers/image/v5@v5.22.0: Get "https://proxy.golang.o
  54. rg/github.com/containers/image/v5/@v/v5.22.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/oci/oci.go:23:2: github.com/containers/image/v5@v5.22.0: Get "https://proxy.golang.o
  55. rg/github.com/containers/image/v5/@v/v5.22.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/sources/conveyorPacker_oci.go:38:2: github.com/containers/image/v5@v5.22.0: Get "htt
  56. ps://proxy.golang.org/github.com/containers/image/v5/@v/v5.22.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/sources/conveyorPacker_oci.go:39:2: github.com/containers/image/v5@v5.22.0: Get "htt
  57. ps://proxy.golang.org/github.com/containers/image/v5/@v/v5.22.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/sources/conveyorPacker_oci.go:40:2: github.com/containers/image/v5@v5.22.0: Get "htt
  58. ps://proxy.golang.org/github.com/containers/image/v5/@v/v5.22.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/oci/oci.go:24:2: github.com/containers/image/v5@v5.22.0: Get "https://proxy.golang.o
  59. rg/github.com/containers/image/v5/@v/v5.22.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/oci/oci.go:25:2: github.com/containers/image/v5@v5.22.0: Get "https://proxy.golang.o
  60. rg/github.com/containers/image/v5/@v/v5.22.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/oci/oci.go:26:2: github.com/containers/image/v5@v5.22.0: Get "https://proxy.golang.o
  61. rg/github.com/containers/image/v5/@v/v5.22.0.zip": dial tcp 172.217.160.113:443: i/o timeout../pkg/build/types/bundle.go:24:2: github.com/containers/image/v5@v5.22.0: Get "https://proxy.golang.org/g
  62. ithub.com/containers/image/v5/@v/v5.22.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/runtime/engine/oci/prepare_linux.go:24:2: github.com/creack/pty@v1.1.18: Get "https://prox
  63. y.golang.org/github.com/creack/pty/@v/v1.1.18.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/files/files.go:19:2: github.com/cyphar/filepath-securejoin@v0.2.3: Get "https://prox
  64. y.golang.org/github.com/cyphar/filepath-securejoin/@v/v0.2.3.zip": dial tcp 172.217.160.113:443: i/o timeout../pkg/util/archive/copy.go:17:2: github.com/docker/docker@v20.10.17+incompatible: Get "https://proxy.gola
  65. ng.org/github.com/docker/docker/@v/v20.10.17+incompatible.zip": dial tcp 172.217.160.113:443: i/o timeout../pkg/util/archive/copy.go:18:2: github.com/docker/docker@v20.10.17+incompatible: Get "https://proxy.gola
  66. ng.org/github.com/docker/docker/@v/v20.10.17+incompatible.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/app/apptainer/instance_linux.go:30:2: github.com/docker/go-units@v0.4.0: Get "https://proxy.go
  67. lang.org/github.com/docker/go-units/@v/v0.4.0.zip": dial tcp 172.217.160.113:443: i/o timeout../cmd/internal/cli/pgp.go:31:2: github.com/fatih/color@v1.13.0: Get "https://proxy.golang.org/github.com/
  68. fatih/color/@v/v1.13.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/remote/endpoint/client.go:21:2: github.com/go-log/log@v0.2.0: Get "https://proxy.golang.or
  69. g/github.com/go-log/log/@v/v0.2.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/util/crypt/crypt_dev.go:28:2: github.com/google/uuid@v1.3.0: Get "https://proxy.golang.org
  70. /github.com/google/uuid/@v/v1.3.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/remote/endpoint/config.go:24:2: github.com/gosimple/slug@v1.12.0: Get "https://proxy.golan
  71. g.org/github.com/gosimple/slug/@v/v1.12.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/client/oras/oras.go:34:2: github.com/opencontainers/go-digest@v1.0.0: Get "https://proxy.g
  72. olang.org/github.com/opencontainers/go-digest/@v/v1.0.0.zip": dial tcp 172.217.160.113:443: i/o timeout../pkg/ocibundle/sif/bundle_linux.go:21:2: github.com/opencontainers/image-spec@v1.0.2-0.20211117181255-69
  73. 3428a734f5: Get "https://proxy.golang.org/github.com/opencontainers/image-spec/@v/v1.0.2-0.20211117181255-693428a734f5.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/cgroups/manager_linux.go:22:2: github.com/opencontainers/runc@v1.1.4: Get "https://proxy.g
  74. olang.org/github.com/opencontainers/runc/@v/v1.1.4.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/cgroups/manager_linux.go:24:2: github.com/opencontainers/runc@v1.1.4: Get "https://proxy.g
  75. olang.org/github.com/opencontainers/runc/@v/v1.1.4.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/cgroups/manager_linux.go:25:2: github.com/opencontainers/runc@v1.1.4: Get "https://proxy.g
  76. olang.org/github.com/opencontainers/runc/@v/v1.1.4.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/cgroups/manager_linux.go:26:2: github.com/opencontainers/runc@v1.1.4: Get "https://proxy.g
  77. olang.org/github.com/opencontainers/runc/@v/v1.1.4.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/runtime/engine/config/oci/generate/generate.go:35:2: github.com/opencontainers/runtime-spe
  78. c@v1.0.3-0.20210326190908-1c3f411f0417: Get "https://proxy.golang.org/github.com/opencontainers/runtime-spec/@v/v1.0.3-0.20210326190908-1c3f411f0417.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/security/selinux/selinux_supported.go:14:8: github.com/opencontainers/selinux@v1.10.1: Get
  79.  "https://proxy.golang.org/github.com/opencontainers/selinux/@v/v1.10.1.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/sources/oci_unpack.go:30:2: github.com/opencontainers/umoci@v0.4.7: Get "https://pro
  80. xy.golang.org/github.com/opencontainers/umoci/@v/v0.4.7.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/sources/oci_unpack.go:31:2: github.com/opencontainers/umoci@v0.4.7: Get "https://pro
  81. xy.golang.org/github.com/opencontainers/umoci/@v/v0.4.7.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/sources/oci_unpack.go:32:2: github.com/opencontainers/umoci@v0.4.7: Get "https://pro
  82. xy.golang.org/github.com/opencontainers/umoci/@v/v0.4.7.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/cgroups/config_linux.go:18:2: github.com/pelletier/go-toml@v1.9.5: Get "https://proxy.gola
  83. ng.org/github.com/pelletier/go-toml/@v/v1.9.5.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/util/bin/bin.go:22:2: github.com/pkg/errors@v0.9.1: Get "https://proxy.golang.org/github.c
  84. om/pkg/errors/@v/v0.9.1.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/runtime/engine/config/oci/config.go:20:2: github.com/seccomp/containers-golang@v0.6.0: Get
  85.  "https://proxy.golang.org/github.com/seccomp/containers-golang/@v/v0.6.0.zip": dial tcp 172.217.160.113:443: i/o timeout../cmd/internal/cli/cgroups.go:21:2: github.com/shopspring/decimal@v1.3.1: Get "https://proxy.golang.org/g
  86. ithub.com/shopspring/decimal/@v/v1.3.1.zip": dial tcp 172.217.160.113:443: i/o timeout../pkg/cmdline/cmd.go:16:2: github.com/spf13/cobra@v1.5.0: Get "https://proxy.golang.org/github.com/spf13/
  87. cobra/@v/v1.5.0.zip": dial tcp 172.217.160.113:443: i/o timeout../pkg/cmdline/env.go:17:2: github.com/spf13/pflag@v1.0.5: Get "https://proxy.golang.org/github.com/spf13/
  88. pflag/@v/v1.0.5.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/remote/endpoint/service.go:24:2: github.com/sylabs/json-resp@v0.8.1: Get "https://proxy.go
  89. lang.org/github.com/sylabs/json-resp/@v/v0.8.1.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/app/apptainer/push.go:27:2: github.com/vbauerster/mpb/v7@v7.4.2: Get "https://proxy.golang.org
  90. /github.com/vbauerster/mpb/v7/@v/v7.4.2.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/app/apptainer/push.go:28:2: github.com/vbauerster/mpb/v7@v7.4.2: Get "https://proxy.golang.org
  91. /github.com/vbauerster/mpb/v7/@v/v7.4.2.zip": dial tcp 172.217.160.113:443: i/o timeout../pkg/util/capabilities/process_linux.go:15:2: golang.org/x/sys@v0.0.0-20220715151400-c0bba94af5f8: Get "
  92. https://proxy.golang.org/golang.org/x/sys/@v/v0.0.0-20220715151400-c0bba94af5f8.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/util/interactive/interactive.go:23:2: golang.org/x/term@v0.0.0-20210927222741-03fcf44c2211
  93. : Get "https://proxy.golang.org/golang.org/x/term/@v/v0.0.0-20210927222741-03fcf44c2211.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/remote/remote.go:27:2: gopkg.in/yaml.v2@v2.4.0: Get "https://proxy.golang.org/gopkg.in/yam
  94. l.v2/@v/v2.4.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/util/shell/interpreter/interpreter.go:25:2: mvdan.cc/sh/v3@v3.5.1: Get "https://proxy.gola
  95. ng.org/mvdan.cc/sh/v3/@v/v3.5.1.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/files/files.go:20:2: mvdan.cc/sh/v3@v3.5.1: Get "https://proxy.golang.org/mvdan.cc/s
  96. h/v3/@v/v3.5.1.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/files/files.go:21:2: mvdan.cc/sh/v3@v3.5.1: Get "https://proxy.golang.org/mvdan.cc/s
  97. h/v3/@v/v3.5.1.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/remote/credential/login_handler.go:20:2: oras.land/oras-go@v1.2.0: Get "https://proxy.gola
  98. ng.org/oras.land/oras-go/@v/v1.2.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/remote/credential/login_handler.go:26:2: oras.land/oras-go@v1.2.0: Get "https://proxy.gola
  99. ng.org/oras.land/oras-go/@v/v1.2.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/client/oras/oras.go:37:2: oras.land/oras-go@v1.2.0: Get "https://proxy.golang.org/oras.lan
  100. d/oras-go/@v/v1.2.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/client/oras/oras.go:38:2: oras.land/oras-go@v1.2.0: Get "https://proxy.golang.org/oras.lan
  101. d/oras-go/@v/v1.2.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/client/oras/oras.go:39:2: oras.land/oras-go@v1.2.0: Get "https://proxy.golang.org/oras.lan
  102. d/oras-go/@v/v1.2.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/client/oras/oras.go:40:2: oras.land/oras-go@v1.2.0: Get "https://proxy.golang.org/oras.lan
  103. d/oras-go/@v/v1.2.0.zip": dial tcp 172.217.160.113:443: i/o timeoutmake: *** [apptainer] Error 1

看起来是编译过程中网络连接失败，造成部分库下载不到，导致编译失败。可以尝试如下方法解决问题：

  1. 检查网络连接是否正常，如果有问题请尝试修复。

  2. 重试编译，因为有时网络问题是暂时的，重试可能就可以解决问题。

  3. 手动下载所需库并放入本地目录，可以避免编译过程中从网络上下载，保证编译成功。

编译过程中产生的中间文件通常在编译命令执行的当前目录下的中间目录，具体目录名称和编译工具有关。

另外，提供一些关于编译失败的通用解决方案：

  1. 检查代码是否有语法错误，修复错误后重试编译。

  2. 检查所需的环境变量和依赖是否已经配置，确保环境正确配置。

  3. 清理编译过程中产生的缓存文件，重新编译。

  4. 查阅相关文档，以了解编译要求和建议的解决方案。

sudo yum install如何安装本地存在的文件

如果您有一个本地存在的 RPM 包，您可以使用以下命令安装它：

sudo yum localinstall <filename>.rpm

non-setuid和setuid是关于Unix系统文件权限的术语。

当一个程序被标记为setuid时，当它被执行时，它的权限将从它的所有者变为它的执行者。这意味着即使普通用户执行了一个以setuid标记的程序，该程序仍将具有更高的权限，以便完成某些任务。

相反，当一个程序被标记为non-setuid时，该程序仅具有它的所有者的权限，即使它被普通用户执行。

因此，在上面的代码中，sudo yum install -y apptainer将安装一个没有setuid标记的版本，而sudo yum install -y apptainer-suid将安装一个以setuid标记的版本。

通常，在安全方面，使用non-setuid版本更安全，因为它仅允许该程序以其所有者的权限运行，而不允许它以执行者的权限运行。然而，如果程序需要更高的权限才能完成任务，则必须使用setuid版本。

sudo yum install -y apptainer这段代码是在执行在Red Hat系列的操作系统（如CentOS、Fedora等）上的软件包安装。

yum是一个在Red Hat系列操作系统上进行软件包管理的工具。它允许安装、升级和删除软件包。

在这个代码中，sudo命令用于在管理员权限下执行命令。yum install -y命令是安装软件包的命令，其中-y选项用于默认回答“是”，以便在没有用户交互的情况下安装软件包。最后，apptainer是要安装的软件包的名称。

安装的软件包将被下载并存储在操作系统的软件仓库中，通常在/var/cache/yum或/var/lib/yum目录下。安装后的文件将安装在系统的文件系统中，通常在/usr/目录下。

  1. Install RPM from EPEL or Fedora
  2. Multiple architectures of RPMs are available for Red Hat Enterprise Linux and Fedora.
  3.  
  4. First, on Red Hat Enterprise Linux derived systems enable the EPEL repositories like this:
  5.  
  6. $ sudo yum install -y epel-release
  7. Then to install a non-setuid installation of Apptainer do:
  8.  
  9. $ sudo yum install -y apptainer
  10. or for a setuid installation do:
  11.  
  12. $ sudo yum install -y apptainer-suid
  13. Install from GitHub release RPMs
  14. Alternatively, x86_64 RPMs are available on GitHub immediately after each Apptainer release and they can be installed directly from there. For the non-setuid installation:
  15.  
  16. $ sudo yum install -y https://github.com/apptainer/apptainer/releases/download/v1.1.5/apptainer-1.1.5-1.x86_64.rpm
  17. For the setuid installation do above command first and then this one:
  18.  
  19. $ sudo yum install -y https://github.com/apptainer/apptainer/releases/download/v1.1.5/apptainer-suid-1.1.5-1.x86_64.rpm

 singularity 安装与使用 - 简书   成功！！

echo 'export PATH=~/.aspera/connect/bin/:$PATH' >> ~/.bashrc
source ~/.bashrc singularity/INSTALL.md at master · apptainer/singularity · GitHub

如何直接使用sigularity 或者apptainer调用软件 virsorter2

Option 3

If you have apptainer (formerly known as singularity) installed (typical in HPC clusters), the following is the most convenient. Also use the option if you have issues with conda.

apptainer build virsorter2.sif docker://jiarong/virsorter:latest

You will get a file virsorter2.sif, which is a singularity image that can be run like a binary executable file. You can use the absolute path of this file to replace virsorter in commands for the rest of the tutorial. Also this image has the database and dependencies included, so you can skip the Download database and dependencies stephttps://github.com/jiarong/VirSorter2#download-database-and-dependencies below.

 singularity使用

  1. singularity build metawrap.sif docker://lmwbio/metawrap_1.3.2_binning_fastq_gz
  2.  
  3.  
  4. INFO:    Starting build...
  5. Getting image source signatures

 sourmash  先安装pip 再用pip安装sourmashGitHub - sourmash-bio/sourmash: Quickly search, compare, and analyze genomic and metagenomic data sets.

Singularity 可以直接从 Docker Hub 下载镜像，您可以使用以下命令：

singularity pull docker://<DOCKER_IMAGE_NAME>:<TAG>

问题1. Singularity 可以直接从 Docker Hub 下载镜像速度太慢，我应该怎么办 问题2. 我可以先把docker镜像下载到本地，然后使用singularity来安装本地的镜像吗？具体应该怎么做

  1. 如果 Singularity 从 Docker Hub 下载镜像速度太慢，您可以尝试以下几种方法：

    • 使用私有镜像仓库，如 Google Container Registry，Amazon Elastic Container Registry，或 Quay.io。
    • 使用更快的网络，例如 VPN 或私有网络。
    • 使用国内的 Docker 镜像仓库，例如 Docker 中国镜像。

  2. 是的，您可以先下载 Docker 镜像到本地，然后使用 Singularity 安装本地的镜像。

具体操作如下：

  • 使用 docker save 命令将镜像存储到本地：

docker save <IMAGE_NAME>:<TAG> -o <SAVE_FILE>.tar

docker save ubuntu:20.04 -o ubuntu_20.04.tar

  • 使用 singularity image.create 命令将存储文件转换为 Singularity 容器：

singularity image.create <SINGULARITY_CONTAINER>.sif

例如：

singularity image.create ubuntu_20.04.sif

  • 使用 singularity import 命令从存储文件导入镜像：

singularity import <SINGULARITY_CONTAINER>.sif <SAVE_FILE>.tar

singularity import ubuntu_20.04.sif ubuntu_20.04.tar

现在，您应该已经有了一个本地的 Singularity 容器，可以快速启动和运行。

windows系统安装dockerInstall on Windows | Docker Documentation

在 Windows 系统中，可以使用 Docker Desktop 软件下载 Docker 镜像。

首先，请确保已安装 Docker Desktop，并已启动 Docker 引擎。

然后，打开命令提示符或 PowerShell，输入以下命令：

docker pull lmwbio/metawrap_1.3.2_binning_fastq_gz

这将下载镜像到您的计算机上，并将其存储在 Docker 镜像库中。

稍后，您可以使用 docker run 命令启动该镜像。

例如：

docker run lmwbio/metawrap_1.3.2_binning_fastq_gz

metaphlan2

https://anaconda.org/bioconda/metaphlan2

 GitHub - biobakery/MetaPhlAn2

metawrap

最终通过把metawrap下载到本地 然后使用conda安装本地软件

conda install --use-local *****

GitHub - bxlab/metaWRAP: MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

container/Singularity.metawrap at master · hexmek/container · GitHub

在 CentOS 系统中安装 metaWRAP 使用 Singularity 可以通过以下步骤进行：

  1. 安装 Singularity：
 
 
Copy code
 
 
sudo yum install singularity 
 
 
  1. 创建一个 Singularity 容器文件，其内容如下：
 
 
 
 
bashCopy code
 
 
Bootstrap: docker From: ubuntu:16.04 %post apt-get update apt-get -y install wget wget https://github.com/bzhangHu/metaWRAP/releases/download/v1.0/metaWRAP-Linux.tar.gz tar -xvzf metaWRAP-Linux.tar.gz rm metaWRAP-Linux.tar.gz 
 
 
  1. 创建 Singularity 容器：
 
 
 
 
pythonCopy code
 
 
sudo singularity build metawrap.sif metawrap.def 
 
 
  1. 运行容器：
 
 
singularity run metawrap.sif 
 
 
这样，您就可以在 Singularity 容器中使用 metaWRAP 了。
 

 

 

 

 

megahit
 

一文详解宏基因组组装工具Megahit安装及应用 - 知乎
 

 

SOAPdenovo2 soapaligner
 

GitHub - aquaskyline/SOAPdenovo2: Next generation sequencing reads de novo assembler.
 

 

各个数据库数据库 | 基因组注释 - 简书
 

vfdb
 

2021.3.17丨致病菌毒力因子（VFDB）数据库注释_穆易青的博客-CSDN博客_vfdb数据库
 

unite its扩增子数据库
 

史上最详细的微生物扩增子数据库整理_刘永鑫Adam的博客-CSDN博客_greengene数据库
 

微生物多样性专题 | 扩增子测序分析实战（二）数据库整理之UNITE

                

        
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