gatk4安装过程

配置环境SLES11PS1, anaconda3
#################################

$ conda create -n gatk419 gatk4
~/anaconda3/lib/python3.6/site-packages/requests/__init__.py:104: RequestsDependencyWarning: urllib3 (1.26.7) or chardet (2.3.0)/charset_normalizer (2.0.9) doesn't match a supported version!
  RequestsDependencyWarning)
Collecting package metadata (current_repodata.json): done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
  current version: 4.10.3
  latest version: 4.14.0

Please update conda by running

    $ conda update -n base conda



## Package Plan ##

  environment location: ~/anaconda3/envs/gatk419

  added / updated specs:
    - gatk4


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    alsa-lib-1.2.6.1           |       h7f98852_0         578 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    ca-certificates-2022.9.14  |       ha878542_0         152 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    fontconfig-2.14.0          |       hc2a2eb6_1         318 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    gatk4-4.2.6.1              |   py36hdfd78af_1       275.7 MB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
    giflib-5.2.1               |       h36c2ea0_2          77 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    lcms2-2.12                 |       hddcbb42_0         443 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    libcups-2.3.3              |       h3e49a29_2         4.5 MB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    libdeflate-1.14            |       h166bdaf_0          81 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    libpng-1.6.38              |       h753d276_0         371 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    libsqlite-3.39.3           |       h753d276_0         789 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    libtiff-4.4.0              |       h55922b4_4         651 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    libzlib-1.2.12             |       h166bdaf_3          65 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    openjdk-11.0.15            |       h1e1ecb3_1       174.1 MB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    xorg-fixesproto-5.0        |    h7f98852_1002           9 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    xorg-inputproto-2.3.2      |    h7f98852_1002          19 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    xorg-libxfixes-5.0.3       |    h7f98852_1004          18 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    xorg-libxi-1.7.10          |       h7f98852_0          46 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    xorg-libxtst-1.2.3         |    h7f98852_1002          31 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    xorg-recordproto-1.14.2    |    h7f98852_1002           8 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    zlib-1.2.12                |       h166bdaf_3          92 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    ------------------------------------------------------------
                                           Total:       458.0 MB


The following NEW packages will be INSTALLED:

  _libgcc_mutex      anaconda/cloud/conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      anaconda/cloud/conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
  alsa-lib           anaconda/cloud/conda-forge/linux-64::alsa-lib-1.2.6.1-h7f98852_0
  bzip2              anaconda/cloud/conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
  ca-certificates    anaconda/cloud/conda-forge/linux-64::ca-certificates-2022.9.14-ha878542_0
  cairo              anaconda/cloud/conda-forge/linux-64::cairo-1.16.0-ha61ee94_1013
  expat              anaconda/cloud/conda-forge/linux-64::expat-2.4.8-h27087fc_0
  font-ttf-dejavu-s~ anaconda/cloud/conda-forge/noarch::font-ttf-dejavu-sans-mono-2.37-hab24e00_0
  font-ttf-inconsol~ anaconda/cloud/conda-forge/noarch::font-ttf-inconsolata-3.000-h77eed37_0
  font-ttf-source-c~ anaconda/cloud/conda-forge/noarch::font-ttf-source-code-pro-2.038-h77eed37_0
  font-ttf-ubuntu    anaconda/cloud/conda-forge/noarch::font-ttf-ubuntu-0.83-hab24e00_0
  fontconfig         anaconda/cloud/conda-forge/linux-64::fontconfig-2.14.0-hc2a2eb6_1
  fonts-conda-ecosy~ anaconda/cloud/conda-forge/noarch::fonts-conda-ecosystem-1-0
  fonts-conda-forge  anaconda/cloud/conda-forge/noarch::fonts-conda-forge-1-0
  freetype           anaconda/cloud/conda-forge/linux-64::freetype-2.12.1-hca18f0e_0
  gatk4              anaconda/cloud/bioconda/noarch::gatk4-4.2.6.1-py36hdfd78af_1
  gettext            anaconda/cloud/conda-forge/linux-64::gettext-0.19.8.1-h73d1719_1008
  giflib             anaconda/cloud/conda-forge/linux-64::giflib-5.2.1-h36c2ea0_2
  graphite2          anaconda/cloud/conda-forge/linux-64::graphite2-1.3.13-h58526e2_1001
  harfbuzz           anaconda/cloud/conda-forge/linux-64::harfbuzz-5.1.0-hf9f4e7c_0
  icu                anaconda/cloud/conda-forge/linux-64::icu-70.1-h27087fc_0
  jpeg               anaconda/cloud/conda-forge/linux-64::jpeg-9e-h166bdaf_2
  keyutils           anaconda/cloud/conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0
  krb5               anaconda/cloud/conda-forge/linux-64::krb5-1.19.3-h08a2579_0
  lcms2              anaconda/cloud/conda-forge/linux-64::lcms2-2.12-hddcbb42_0
  ld_impl_linux-64   anaconda/cloud/conda-forge/linux-64::ld_impl_linux-64-2.36.1-hea4e1c9_2
  lerc               anaconda/cloud/conda-forge/linux-64::lerc-4.0.0-h27087fc_0
  libcups            anaconda/cloud/conda-forge/linux-64::libcups-2.3.3-h3e49a29_2
  libdeflate         anaconda/cloud/conda-forge/linux-64::libdeflate-1.14-h166bdaf_0
  libedit            anaconda/cloud/conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
  libffi             anaconda/cloud/conda-forge/linux-64::libffi-3.4.2-h7f98852_5
  libgcc-ng          anaconda/cloud/conda-forge/linux-64::libgcc-ng-12.1.0-h8d9b700_16
  libglib            anaconda/cloud/conda-forge/linux-64::libglib-2.72.1-h2d90d5f_0
  libgomp            anaconda/cloud/conda-forge/linux-64::libgomp-12.1.0-h8d9b700_16
  libiconv           anaconda/cloud/conda-forge/linux-64::libiconv-1.16-h516909a_0
  libnsl             anaconda/cloud/conda-forge/linux-64::libnsl-2.0.0-h7f98852_0
  libpng             anaconda/cloud/conda-forge/linux-64::libpng-1.6.38-h753d276_0
  libsqlite          anaconda/cloud/conda-forge/linux-64::libsqlite-3.39.3-h753d276_0
  libstdcxx-ng       anaconda/cloud/conda-forge/linux-64::libstdcxx-ng-12.1.0-ha89aaad_16
  libtiff            anaconda/cloud/conda-forge/linux-64::libtiff-4.4.0-h55922b4_4
  libuuid            anaconda/cloud/conda-forge/linux-64::libuuid-2.32.1-h7f98852_1000
  libwebp-base       anaconda/cloud/conda-forge/linux-64::libwebp-base-1.2.4-h166bdaf_0
  libxcb             anaconda/cloud/conda-forge/linux-64::libxcb-1.13-h7f98852_1004
  libzlib            anaconda/cloud/conda-forge/linux-64::libzlib-1.2.12-h166bdaf_3
  ncurses            anaconda/cloud/conda-forge/linux-64::ncurses-6.3-h27087fc_1
  openjdk            anaconda/cloud/conda-forge/linux-64::openjdk-11.0.15-h1e1ecb3_1
  openssl            anaconda/cloud/conda-forge/linux-64::openssl-3.0.5-h166bdaf_2
  pcre               anaconda/cloud/conda-forge/linux-64::pcre-8.45-h9c3ff4c_0
  pip                anaconda/cloud/conda-forge/noarch::pip-22.2.2-pyhd8ed1ab_0
  pixman             anaconda/cloud/conda-forge/linux-64::pixman-0.40.0-h36c2ea0_0
  pthread-stubs      anaconda/cloud/conda-forge/linux-64::pthread-stubs-0.4-h36c2ea0_1001
  python             anaconda/cloud/conda-forge/linux-64::python-3.10.6-ha86cf86_0_cpython
  readline           anaconda/cloud/conda-forge/linux-64::readline-8.1.2-h0f457ee_0
  setuptools         anaconda/cloud/conda-forge/noarch::setuptools-65.3.0-pyhd8ed1ab_1
  tk                 anaconda/cloud/conda-forge/linux-64::tk-8.6.12-h27826a3_0
  tzdata             anaconda/cloud/conda-forge/noarch::tzdata-2022c-h191b570_0
  wheel              anaconda/cloud/conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
  xorg-fixesproto    anaconda/cloud/conda-forge/linux-64::xorg-fixesproto-5.0-h7f98852_1002
  xorg-inputproto    anaconda/cloud/conda-forge/linux-64::xorg-inputproto-2.3.2-h7f98852_1002
  xorg-kbproto       anaconda/cloud/conda-forge/linux-64::xorg-kbproto-1.0.7-h7f98852_1002
  xorg-libice        anaconda/cloud/conda-forge/linux-64::xorg-libice-1.0.10-h7f98852_0
  xorg-libsm         anaconda/cloud/conda-forge/linux-64::xorg-libsm-1.2.3-hd9c2040_1000
  xorg-libx11        anaconda/cloud/conda-forge/linux-64::xorg-libx11-1.7.2-h7f98852_0
  xorg-libxau        anaconda/cloud/conda-forge/linux-64::xorg-libxau-1.0.9-h7f98852_0
  xorg-libxdmcp      anaconda/cloud/conda-forge/linux-64::xorg-libxdmcp-1.1.3-h7f98852_0
  xorg-libxext       anaconda/cloud/conda-forge/linux-64::xorg-libxext-1.3.4-h7f98852_1
  xorg-libxfixes     anaconda/cloud/conda-forge/linux-64::xorg-libxfixes-5.0.3-h7f98852_1004
  xorg-libxi         anaconda/cloud/conda-forge/linux-64::xorg-libxi-1.7.10-h7f98852_0
  xorg-libxrender    anaconda/cloud/conda-forge/linux-64::xorg-libxrender-0.9.10-h7f98852_1003
  xorg-libxtst       anaconda/cloud/conda-forge/linux-64::xorg-libxtst-1.2.3-h7f98852_1002
  xorg-recordproto   anaconda/cloud/conda-forge/linux-64::xorg-recordproto-1.14.2-h7f98852_1002
  xorg-renderproto   anaconda/cloud/conda-forge/linux-64::xorg-renderproto-0.11.1-h7f98852_1002
  xorg-xextproto     anaconda/cloud/conda-forge/linux-64::xorg-xextproto-7.3.0-h7f98852_1002
  xorg-xproto        anaconda/cloud/conda-forge/linux-64::xorg-xproto-7.0.31-h7f98852_1007
  xz                 anaconda/cloud/conda-forge/linux-64::xz-5.2.6-h166bdaf_0
  zlib               anaconda/cloud/conda-forge/linux-64::zlib-1.2.12-h166bdaf_3
  zstd               anaconda/cloud/conda-forge/linux-64::zstd-1.5.2-h6239696_4


Proceed ([y]/n)?


Downloading and Extracting Packages
zlib-1.2.12          | 92 KB     | ############################################################################ | 100%
lcms2-2.12           | 443 KB    | ############################################################################ | 100%
xorg-inputproto-2.3. | 19 KB     | ############################################################################ | 100%
libpng-1.6.38        | 371 KB    | ############################################################################ | 100%
xorg-libxtst-1.2.3   | 31 KB     | ############################################################################ | 100%
libcups-2.3.3        | 4.5 MB    | ############################################################################ | 100%
libsqlite-3.39.3     | 789 KB    | ############################################################################ | 100%
openjdk-11.0.15      | 174.1 MB  | ############################################################################ | 100%
alsa-lib-1.2.6.1     | 578 KB    | ############################################################################ | 100%
xorg-libxfixes-5.0.3 | 18 KB     | ############################################################################ | 100%
xorg-libxi-1.7.10    | 46 KB     | ############################################################################ | 100%
fontconfig-2.14.0    | 318 KB    | ############################################################################ | 100%
xorg-fixesproto-5.0  | 9 KB      | ############################################################################ | 100%
xorg-recordproto-1.1 | 8 KB      | ############################################################################ | 100%
ca-certificates-2022 | 152 KB    | ############################################################################ | 100%
libtiff-4.4.0        | 651 KB    | ############################################################################ | 100%
gatk4-4.2.6.1        | 275.7 MB  | ############################################################################ | 100%
giflib-5.2.1         | 77 KB     | ############################################################################ | 100%
libdeflate-1.14      | 81 KB     | ############################################################################ | 100%
libzlib-1.2.12       | 65 KB     | ############################################################################ | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate gatk419
#
# To deactivate an active environment, use
#
#     $ conda deactivate

之后激活gatk419环境

#当使用conda activate gatk419激活不成功时，可在此之前运行一下命令
#source ~/anaconda3/etc/profile.d/conda.sh
$ conda activate gatk419

之后就进入了创建的环境中，在创建的环境中安装bowtie2, bwa, fastap等你 需要的软件。
安装bowtie2

(gatk419) jiangtao@node17:~>   conda install bowtie2

Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.10.3
  latest version: 4.14.0

Please update conda by running

    $ conda update -n base conda



## Package Plan ##

  environment location: ~/anaconda3/envs/gatk419

  added / updated specs:
    - bowtie2


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    bowtie2-2.4.5              |  py310h8d7afc0_4        14.4 MB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
    python_abi-3.10            |          2_cp310           4 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    tbb-2021.5.0               |       h924138e_2         1.9 MB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    ------------------------------------------------------------
                                           Total:        16.3 MB

The following NEW packages will be INSTALLED:

  bowtie2            anaconda/cloud/bioconda/linux-64::bowtie2-2.4.5-py310h8d7afc0_4
  perl               anaconda/cloud/conda-forge/linux-64::perl-5.32.1-2_h7f98852_perl5
  python_abi         anaconda/cloud/conda-forge/linux-64::python_abi-3.10-2_cp310
  tbb                anaconda/cloud/conda-forge/linux-64::tbb-2021.5.0-h924138e_2


Proceed ([y]/n)?


Downloading and Extracting Packages
tbb-2021.5.0         | 1.9 MB    | ############################################################################ | 100%
python_abi-3.10      | 4 KB      | ############################################################################ | 100%
bowtie2-2.4.5        | 14.4 MB   | ############################################################################ | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(gatk419) jiangtao@node17:~>
(gatk419) jiangtao@node17:~> conda install bwa
~/anaconda3/lib/python3.6/site-packages/requests/__init__.py:104: RequestsDependencyWarning: urllib3 (1.26.7) or chardet (2.3.0)/charset_normalizer (2.0.9) doesn't match a supported version!
  RequestsDependencyWarning)
Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.10.3
  latest version: 4.14.0

Please update conda by running

    $ conda update -n base conda



## Package Plan ##

  environment location: ~/anaconda3/envs/gatk419

  added / updated specs:
    - bwa


The following NEW packages will be INSTALLED:

  bwa                anaconda/cloud/bioconda/linux-64::bwa-0.7.17-h7132678_9


Proceed ([y]/n)?

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

安装bwa

(gatk419) jiangtao@node17:~> conda install bwa

Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.10.3
  latest version: 4.14.0

Please update conda by running

    $ conda update -n base conda



## Package Plan ##

  environment location: ~/anaconda3/envs/gatk419

  added / updated specs:
    - bwa


The following NEW packages will be INSTALLED:

  bwa                anaconda/cloud/bioconda/linux-64::bwa-0.7.17-h7132678_9


Proceed ([y]/n)?

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

安装fastp

(gatk419) jiangtao@node17:~> conda install fastp

Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.10.3
  latest version: 4.14.0

Please update conda by running

    $ conda update -n base conda



## Package Plan ##

  environment location: ~/anaconda3/envs/gatk419

  added / updated specs:
    - fastp


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    fastp-0.23.2               |       h5f740d0_3         3.2 MB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
    isa-l-2.30.0               |       ha770c72_4         192 KB  http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    ------------------------------------------------------------
                                           Total:         3.4 MB

The following NEW packages will be INSTALLED:

  fastp              anaconda/cloud/bioconda/linux-64::fastp-0.23.2-h5f740d0_3
  isa-l              anaconda/cloud/conda-forge/linux-64::isa-l-2.30.0-ha770c72_4

The following packages will be DOWNGRADED:

  libdeflate                                1.14-h166bdaf_0 --> 1.13-h166bdaf_0
  libtiff                                  4.4.0-h55922b4_4 --> 4.4.0-h0e0dad5_3


Proceed ([y]/n)?


Downloading and Extracting Packages
isa-l-2.30.0         | 192 KB    | ############################################################################ | 100%
fastp-0.23.2         | 3.2 MB    | ############################################################################ | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

整体过程还算比较顺利，没有碰到太大问题。
配置完成之后，之后再使用这些软件时，可以通过激活gatk419环境即可。
一般使用conda activate gatk419即可激活。
如果不成功，就再运行一条命令
source ~/anaconda3/etc/profile.d/conda.sh
之后，再运行conda activate gatk419即可激活

©著作权归作者所有,转载或内容合作请联系作者
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