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