"conda activate" can't activate or switch environments during a job submitted to a queuing system, even though passing full environment_variables. #8536
Description
I am working on my Institutes Unix_Cluster, which employs slurm as a job-queing system. Since some tools i want to use within a pipline have incompatible dependencies, i sometimes have to switch between conda environments during the workflow, or at least make sure that the correct environment is active during the current job.. This is a problem when submitting jobs as bash-scripts to a Job submission system on a server (in our case slurm with moab).
As long as i pass my current environment-variables to the submission system (e.g. using the "-V" flag in the case of moab), the jobs work fine as long as i was currently in the correct environment, when i submitted them.
However, if i try to ensure the correct environment in the script (or try to switch environments in between) by adding, e.g., conda activate myother_env within the script, i get the following error:
CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run
$ conda init <SHELL_NAME>
Apparently, even though i pass my environmental variables to the submission system, conda needs to modify setting files on the servers the job actually gets sent to. However, can't just modify any setting files there...
Current Behavior
When submitting a job to slurm in the form of a bash script (while also passing all my current environment variables), containing the following line: conda activate myother_env, I get an error (CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.)
Steps to Reproduce
Create a bash script that at some point contains the line:
conda activate <my_env>
Submit the job to a job-submission system such as slurm
Expected Behavior
The conda environment should switch to the selected environment
Environment Information
`conda info`
active environment : py27_env
active env location : /home/kit/ibg/ww5070/tools/miniconda2/envs/py27_env
shell level : 1
user config file : /home/kit/ibg/ww5070/.condarc
populated config files : /home/kit/ibg/ww5070/.condarc
conda version : 4.6.7
conda-build version : not installed
python version : 2.7.15.final.0
base environment : /home/kit/ibg/ww5070/tools/miniconda2 (writable)
channel URLs : https://conda.anaconda.org/bioconda/linux-64
https://conda.anaconda.org/bioconda/noarch
https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/free/linux-64
https://repo.anaconda.com/pkgs/free/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
https://conda.anaconda.org/r/linux-64
https://conda.anaconda.org/r/noarch
package cache : /home/kit/ibg/ww5070/tools/miniconda2/pkgs
/home/kit/ibg/ww5070/.conda/pkgs
envs directories : /home/kit/ibg/ww5070/tools/miniconda2/envs
/home/kit/ibg/ww5070/.conda/envs
platform : linux-64
user-agent : conda/4.6.7 requests/2.18.4 CPython/2.7.15 Linux/3.10.0-862.14.4.el7.x86_64 rhel/7.6 glibc/2.17
UID:GID : 225783:44422
netrc file : None
offline mode : False
`conda config --show-sources`
==> /home/kit/ibg/ww5070/.condarc <==
channels:
- bioconda
- conda-forge
- defaults
- r
`conda list --show-channel-urls`
# packages in environment at /home/kit/ibg/ww5070/tools/miniconda2/envs/py27_env:
#
# Name Version Build Channel
_r-mutex 1.0.0 anacondar_1 defaults
aragorn 1.2.38 h470a237_2 bioconda
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.5 py_1 conda-forge
backports_abc 0.5 py_1 conda-forge
barrnap 0.9 2 bioconda
bbmap 38.22 h14c3975_1 bioconda
bcftools 1.9 h47928c2_1 bioconda
bedtools 2.27.1 he860b03_3 bioconda
binutils_impl_linux-64 2.31.1 h6176602_1 conda-forge
binutils_linux-64 2.31.1 h6176602_3 conda-forge
biopython 1.70 np112py27_1 bioconda
blas 1.0 mkl defaults
blast 2.7.1 h4422958_6 bioconda
boost 1.67.0 py27h3e44d54_0 conda-forge
boost-cpp 1.67.0 h3a22d5f_0 conda-forge
bowtie2 2.3.4.3 py27he860b03_1 bioconda
bwidget 1.9.11 1 defaults
bz2file 0.98 py_0 conda-forge
bzip2 1.0.6 h14c3975_1002 conda-forge
ca-certificates 2019.3.9 hecc5488_0 conda-forge
cairo 1.14.12 h80bd089_1005 conda-forge
certifi 2019.3.9 py27_0 conda-forge
checkm-genome 1.0.13 py27_0 bioconda
clustalw 2.1 h6bb024c_3 bioconda
concoct 1.0.0 py27h63c6309_2 bioconda
curl 7.62.0 hbc83047_0 defaults
cutadapt 1.18 py27h14c3975_1 bioconda
cycler 0.10.0 py_1 conda-forge
cython 0.29.5 py27hf484d3e_0 conda-forge
dbus 1.13.2 h714fa37_1 defaults
dendropy 4.4.0 py_0 bioconda
diamond 0.9.24 ha87ae23_0 bioconda
expat 2.2.5 hf484d3e_1002 conda-forge
flash 1.2.11 h84994c4_3 bioconda
fontconfig 2.13.1 h2176d3f_1000 conda-forge
fraggenescan 1.31 h470a237_0 bioconda
freetype 2.9.1 h94bbf69_1005 conda-forge
functools32 3.2.3.2 py_3 conda-forge
futures 3.2.0 py27_1000 conda-forge
gcc_impl_linux-64 7.3.0 habb00fd_1 conda-forge
gcc_linux-64 7.3.0 h553295d_3 conda-forge
gettext 0.19.8.1 h9745a5d_1001 conda-forge
gfortran_impl_linux-64 7.3.0 hdf63c60_1 conda-forge
gfortran_linux-64 7.3.0 h553295d_3 conda-forge
giflib 5.1.4 h14c3975_1001 conda-forge
glib 2.56.2 had28632_1001 conda-forge
gmp 6.1.2 hf484d3e_1000 conda-forge
gnutls 3.5.19 h2a4e5f8_1 conda-forge
graphite2 1.3.13 hf484d3e_1000 conda-forge
graphviz 2.38.0 hcf1ce16_1009 conda-forge
gsl 2.2.1 h0c605f7_3 defaults
gst-plugins-base 1.14.0 hbbd80ab_1 defaults
gstreamer 1.14.0 hb453b48_1 defaults
gxx_impl_linux-64 7.3.0 hdf63c60_1 conda-forge
gxx_linux-64 7.3.0 h553295d_3 conda-forge
harfbuzz 1.9.0 he243708_1001 conda-forge
hmmer 3.2.1 hf484d3e_1 bioconda
hmmer2 2.3.2 h470a237_3 bioconda
htslib 1.9 h47928c2_5 bioconda
icu 58.2 hf484d3e_1000 conda-forge
idba 1.1.3 1 bioconda
infernal 1.1.2 h14c3975_2 bioconda
intel-openmp 2019.1 144 defaults
jpeg 9c h14c3975_1001 conda-forge
kiwisolver 1.0.1 py27h6bb024c_1002 conda-forge
krb5 1.14.6 0 conda-forge
libcurl 7.62.0 h20c2e04_0 defaults
libdb 6.1.26 0 bioconda
libdeflate 1.0 h14c3975_1 bioconda
libedit 3.1.20170329 hf8c457e_1001 conda-forge
libffi 3.2.1 hf484d3e_1005 conda-forge
libgcc 7.2.0 h69d50b8_2 conda-forge
libgcc-ng 7.3.0 hdf63c60_0 conda-forge
libgd 2.2.5 h0d07dcb_1005 conda-forge
libgfortran 3.0.0 1 conda-forge
libgfortran-ng 7.3.0 hdf63c60_0 defaults
libiconv 1.15 h14c3975_1004 conda-forge
libidn11 1.33 0 conda-forge
libpng 1.6.36 h84994c4_1000 conda-forge
libssh2 1.8.0 1 conda-forge
libstdcxx-ng 7.3.0 hdf63c60_0 conda-forge
libtiff 4.0.10 h648cc4a_1001 conda-forge
libtool 2.4.6 h14c3975_1002 conda-forge
libuuid 2.32.1 h14c3975_1000 conda-forge
libwebp 1.0.2 h576950b_1 conda-forge
libxcb 1.13 h14c3975_1002 conda-forge
libxml2 2.9.8 h143f9aa_1005 conda-forge
libxslt 1.1.32 h4785a14_1002 conda-forge
llvm-meta 7.0.0 0 conda-forge
make 4.2.1 h14c3975_2004 conda-forge
matplotlib 2.2.3 py27h8a2030e_1 conda-forge
matplotlib-base 2.2.3 py27h60b886d_1 conda-forge
maxbin2 2.2.6 h14c3975_0 bioconda
megahit 1.1.3 py27_0 bioconda
metabat2 2.12.1 0 bioconda
minced 0.3.2 0 bioconda
mkl 2018.0.3 1 defaults
mmtf-python 1.0.2 py27_0 bioconda
msgpack-python 0.6.1 py27h6bb024c_0 conda-forge
muscle 3.8.1551 h6bb024c_4 bioconda
ncurses 6.1 hf484d3e_1002 conda-forge
nettle 3.3 0 conda-forge
nose 1.3.7 py27_1002 conda-forge
numpy 1.12.1 py27h9378851_1 defaults
olefile 0.46 py_0 conda-forge
openblas 0.3.3 ha44fe06_1 conda-forge
openjdk 11.0.1 h14c3975_1014 conda-forge
openmp 7.0.0 h2d50403_0 conda-forge
openssl 1.1.1b h14c3975_1 conda-forge
paml 4.9 h14c3975_4 bioconda
pandas 0.24.1 py27hf484d3e_0 conda-forge
pango 1.40.14 hf0c64fd_1003 conda-forge
parallel 20190122 0 conda-forge
pcre 8.42 h439df22_0 defaults
perl 5.26.2 h14c3975_1001 conda-forge
perl-aceperl 1.92 pl526_2 bioconda
perl-algorithm-diff 1.1903 pl526_2 bioconda
perl-algorithm-munkres 0.08 pl526_1 bioconda
perl-apache-test 1.40 pl526_1 bioconda
perl-app-cpanminus 1.7044 pl526_1 bioconda
perl-appconfig 1.71 pl526_1 bioconda
perl-archive-tar 2.32 pl526_0 bioconda
perl-array-compare 3.0.1 pl526_1 bioconda
perl-autoloader 5.74 pl526_1 bioconda
perl-base 2.23 pl526_1 bioconda
perl-bio-asn1-entrezgene 1.73 pl526_0 bioconda
perl-bio-coordinate 1.007001 pl526_0 bioconda
perl-bio-featureio 1.6.905 pl526_1 bioconda
perl-bio-phylo 0.58 pl526_1 bioconda
perl-bio-samtools 1.43 pl526h1341992_1 bioconda
perl-bio-tools-phylo-paml 1.7.3 pl526_0 bioconda
perl-bio-tools-run-alignment-clustalw 1.7.4 pl526_0 bioconda
perl-bio-tools-run-alignment-tcoffee 1.7.4 pl526_0 bioconda
perl-bioperl 1.7.2 pl526_8 bioconda
perl-bioperl-core 1.7.2 pl526_3 bioconda
perl-bioperl-run 1.007002 pl526_3 bioconda
perl-business-isbn 3.004 pl526_0 bioconda
perl-business-isbn-data 20140910.003 pl526_0 bioconda
perl-cache-cache 1.08 pl526_0 bioconda
perl-capture-tiny 0.48 pl526_0 bioconda
perl-carp 1.38 pl526_1 bioconda
perl-cgi 4.40 pl526h470a237_0 bioconda
perl-class-data-inheritable 0.08 pl526_1 bioconda
perl-class-inspector 1.32 pl526_0 bioconda
perl-class-load 0.25 pl526_0 bioconda
perl-class-load-xs 0.10 pl526h2d50403_0 bioconda
perl-class-method-modifiers 2.12 pl526_0 bioconda
perl-clone 0.41 pl526h470a237_0 bioconda
perl-common-sense 3.74 pl526_2 bioconda
perl-compress-raw-bzip2 2.084 pl526hfc679d8_0 bioconda
perl-compress-raw-zlib 2.084 pl526h2d50403_0 bioconda
perl-constant 1.33 pl526_1 bioconda
perl-convert-binary-c 0.78 pl526h2d50403_2 bioconda
perl-convert-binhex 1.125 pl526_1 bioconda
perl-crypt-rc4 2.02 pl526_1 bioconda
perl-data-dumper 2.173 pl526_0 bioconda
perl-data-optlist 0.110 pl526_2 bioconda
perl-data-stag 0.14 pl526_1 bioconda
perl-date-format 2.30 pl526_1 bioconda
perl-db-file 1.843 pl526h470a237_0 bioconda
perl-dbd-sqlite 1.60 pl526h470a237_0 bioconda
perl-dbi 1.642 pl526_0 bioconda
perl-devel-globaldestruction 0.14 pl526_0 bioconda
perl-devel-overloadinfo 0.005 pl526_0 bioconda
perl-devel-stacktrace 2.03 pl526_1 bioconda
perl-digest-hmac 1.03 pl526_2 bioconda
perl-digest-md5 2.55 pl526_0 bioconda
perl-digest-perl-md5 1.9 pl526_1 bioconda
perl-digest-sha1 2.13 pl526h2d50403_0 bioconda
perl-dist-checkconflicts 0.11 pl526_2 bioconda
perl-dynaloader 1.25 pl526_1 bioconda
perl-email-date-format 1.005 pl526_1 bioconda
perl-encode 2.88 pl526_1 bioconda
perl-encode-locale 1.05 pl526_6 bioconda
perl-error 0.17027 pl526_0 bioconda
perl-eval-closure 0.14 pl526h2d50403_3 bioconda
perl-exception-class 1.44 pl526_0 bioconda
perl-exporter 5.72 pl526_1 bioconda
perl-exporter-tiny 1.002001 pl526_0 bioconda
perl-extutils-makemaker 7.34 pl526_3 bioconda
perl-file-listing 6.04 pl526_1 bioconda
perl-file-path 2.15 pl526_0 bioconda
perl-file-slurp-tiny 0.004 pl526_1 bioconda
perl-file-sort 1.01 pl526_2 bioconda
perl-file-temp 0.2304 pl526_2 bioconda
perl-file-which 1.23 pl526_0 bioconda
perl-font-afm 1.20 pl526_2 bioconda
perl-font-ttf 1.06 pl526_0 bioconda
perl-gd 2.70 pl526he941832_0 bioconda
perl-getopt-long 2.50 pl526_1 bioconda
perl-graph 0.9704 pl526_1 bioconda
perl-graphviz 2.24 pl526h734ff71_0 bioconda
perl-html-element-extended 1.18 pl526_1 bioconda
perl-html-entities-numbered 0.04 pl526_1 bioconda
perl-html-formatter 2.16 pl526_0 bioconda
perl-html-parser 3.72 pl526h2d50403_4 bioconda
perl-html-tableextract 2.13 pl526_2 bioconda
perl-html-tagset 3.20 pl526_3 bioconda
perl-html-tidy 1.60 pl526_0 bioconda
perl-html-tree 5.07 pl526_0 bioconda
perl-html-treebuilder-xpath 0.14 pl526_1 bioconda
perl-http-cookies 6.04 pl526_0 bioconda
perl-http-daemon 6.01 pl526_1 bioconda
perl-http-date 6.02 pl526_3 bioconda
perl-http-message 6.18 pl526_0 bioconda
perl-http-negotiate 6.01 pl526_2 bioconda
perl-image-info 1.38 pl526_1 bioconda
perl-image-size 3.300 pl526_2 bioconda
perl-importer 0.025 pl526_0 bioconda
perl-io-compress 2.084 pl526hfc679d8_0 bioconda
perl-io-html 1.001 pl526_2 bioconda
perl-io-sessiondata 1.03 pl526_1 bioconda
perl-io-socket-ssl 2.060 pl526_0 bioconda
perl-io-string 1.08 pl526_3 bioconda
perl-io-stringy 2.111 pl526_1 bioconda
perl-io-tty 1.12 pl526_1 bioconda
perl-io-zlib 1.10 pl526_2 bioconda
perl-ipc-run 20180523.0 pl526_0 bioconda
perl-ipc-sharelite 0.17 pl526h2d50403_0 bioconda
perl-jcode 2.07 pl526_1 bioconda
perl-json 4.00 pl526_0 bioconda
perl-json-xs 2.34 pl526h2d50403_2 bioconda
perl-lib 0.63 pl526_1 bioconda
perl-libwww-perl 6.36 pl526_0 bioconda
perl-libxml-perl 0.08 pl526_2 bioconda
perl-list-moreutils 0.428 pl526_1 bioconda
perl-list-moreutils-xs 0.428 pl526_0 bioconda
perl-lwp-mediatypes 6.02 pl526_3 bioconda
perl-lwp-protocol-https 6.07 pl526_4 bioconda
perl-lwp-simple 6.15 pl526h470a237_4 bioconda
perl-mailtools 2.20 pl526_0 bioconda
perl-math-cdf 0.1 pl526h470a237_4 bioconda
perl-math-derivative 1.01 pl526_0 bioconda
perl-math-random 0.72 pl526_1 bioconda
perl-math-spline 0.02 pl526_2 bioconda
perl-mime-base64 3.15 pl526_1 bioconda
perl-mime-lite 3.030 pl526_1 bioconda
perl-mime-tools 5.508 pl526_0 bioconda
perl-mime-types 2.17 pl526_0 bioconda
perl-mldbm 2.05 pl526_1 bioconda
perl-module-implementation 0.09 pl526_2 bioconda
perl-module-pluggable 5.2 pl526_0 bioconda
perl-module-runtime 0.016 pl526_0 bioconda
perl-module-runtime-conflicts 0.003 pl526_0 bioconda
perl-moo 2.003004 pl526_0 bioconda
perl-moose 2.2011 pl526h2d50403_0 bioconda
perl-mozilla-ca 20180117 pl526_0 bioconda
perl-mro-compat 0.13 pl526_0 bioconda
perl-net-http 6.18 pl526_0 bioconda
perl-net-ssleay 1.74 0 bioconda
perl-ntlm 1.09 pl526_3 bioconda
perl-ole-storage_lite 0.19 pl526_2 bioconda
perl-package-deprecationmanager 0.17 pl526_0 bioconda
perl-package-stash 0.38 pl526hfc679d8_0 bioconda
perl-package-stash-xs 0.28 pl526hfc679d8_0 bioconda
perl-params-util 1.07 pl526h2d50403_3 bioconda
perl-parent 0.236 pl526_1 bioconda
perl-parse-recdescent 1.967015 pl526_0 bioconda
perl-pathtools 3.73 h470a237_2 bioconda
perl-pdf-api2 2.033 pl526_0 bioconda
perl-pod-escapes 1.07 pl526_1 bioconda
perl-pod-usage 1.69 pl526_1 bioconda
perl-postscript 0.06 pl526_2 bioconda
perl-role-tiny 2.000006 pl526_0 bioconda
perl-scalar-list-utils 1.45 pl526h470a237_3 bioconda
perl-scope-guard 0.21 pl526_2 bioconda
perl-set-scalar 1.29 pl526_2 bioconda
perl-soap-lite 1.19 pl526_1 bioconda
perl-socket 2.027 pl526_1 bioconda
perl-sort-naturally 1.03 pl526_1 bioconda
perl-spreadsheet-parseexcel 0.65 pl526_2 bioconda
perl-spreadsheet-writeexcel 2.40 pl526_1 bioconda
perl-statistics-descriptive 3.0702 pl526_0 bioconda
perl-storable 3.11 pl526_0 bioconda
perl-sub-exporter 0.987 pl526_2 bioconda
perl-sub-exporter-progressive 0.001013 pl526_0 bioconda
perl-sub-identify 0.12 pl526_1 bioconda
perl-sub-info 0.002 pl526_0 bioconda
perl-sub-install 0.928 pl526_2 bioconda
perl-sub-name 0.21 pl526_1 bioconda
perl-sub-quote 2.005001 pl526_0 bioconda
perl-sub-uplevel 0.2800 pl526h470a237_0 bioconda
perl-svg 2.84 pl526_0 bioconda
perl-svg-graph 0.02 pl526_2 bioconda
perl-task-weaken 1.06 pl526_0 bioconda
perl-template-toolkit 2.26 pl526_1 bioconda
perl-term-table 0.013 pl526_0 bioconda
perl-test 1.26 pl526_1 bioconda
perl-test-deep 1.128 pl526_0 bioconda
perl-test-differences 0.64 pl526_2 bioconda
perl-test-exception 0.43 pl526_2 bioconda
perl-test-harness 3.42 pl526_0 bioconda
perl-test-leaktrace 0.16 pl526_1 bioconda
perl-test-more 1.001002 pl526_1 bioconda
perl-test-most 0.35 pl526_0 bioconda
perl-test-requiresinternet 0.05 pl526_0 bioconda
perl-test-warn 0.36 pl526_0 bioconda
perl-test2-suite 0.000117 pl526_0 bioconda
perl-text-diff 1.45 pl526_0 bioconda
perl-threaded 5.22.0 13 bioconda
perl-tie-ixhash 1.23 pl526_2 bioconda
perl-time-hires 1.9758 pl526_0 bioconda
perl-time-local 1.28 pl526_1 bioconda
perl-timedate 2.30 pl526_1 bioconda
perl-tree-dag_node 1.31 pl526_0 bioconda
perl-try-tiny 0.30 pl526_0 bioconda
perl-type-tiny 1.004004 pl526_0 bioconda
perl-types-serialiser 1.0 pl526_2 bioconda
perl-unicode-map 0.112 pl526h2d50403_2 bioconda
perl-uri 1.76 pl526_0 bioconda
perl-www-robotrules 6.02 pl526_3 bioconda
perl-xml-dom 1.46 pl526_0 bioconda
perl-xml-dom-xpath 0.14 pl526_1 bioconda
perl-xml-filter-buffertext 1.01 pl526_2 bioconda
perl-xml-libxml 2.0132 pl526hbc14f71_0 bioconda
perl-xml-libxslt 1.94 pl526_1 bioconda
perl-xml-namespacesupport 1.12 pl526_0 bioconda
perl-xml-parser 2.44 pl526h3a4f0e9_6 bioconda
perl-xml-regexp 0.04 pl526_2 bioconda
perl-xml-sax 1.00 pl526_0 bioconda
perl-xml-sax-base 1.09 pl526_0 bioconda
perl-xml-sax-expat 0.51 pl526_2 bioconda
perl-xml-sax-writer 0.57 pl526_0 bioconda
perl-xml-simple 2.25 pl526_0 bioconda
perl-xml-twig 3.52 pl526_1 bioconda
perl-xml-writer 0.625 pl526_2 bioconda
perl-xml-xpath 1.44 pl526_0 bioconda
perl-xml-xpathengine 0.14 pl526_2 bioconda
perl-xsloader 0.24 pl526_0 bioconda
perl-yaml 1.27 pl526_0 bioconda
pigz 2.3.4 0 conda-forge
pillow 5.4.1 py27h00a061d_1000 conda-forge
pip 19.0.2 py27_0 conda-forge
pixman 0.34.0 h14c3975_1003 conda-forge
pplacer 1.1.alpha19 1 bioconda
prodigal 2.6.3 1 bioconda
prokka 1.13.4 pl526_0 bioconda
pthread-stubs 0.4 h14c3975_1001 conda-forge
pyparsing 2.3.1 py_0 conda-forge
pyqt 5.6.0 py27h13b7fb3_1008 conda-forge
pysam 0.15.2 py27h1671916_1 bioconda
python 2.7.15 h9bab390_6 defaults
python-dateutil 2.8.0 py_0 conda-forge
pytz 2018.9 py_0 conda-forge
qt 5.6.3 h8bf5577_3 defaults
r 3.2.2 0 defaults
r-base 3.2.2 0 r
r-bitops 1.0_6 r3.2.2_1a defaults
r-boot 1.3_17 r3.2.2_0a defaults
r-catools 1.17.1 r3.2.2_2a defaults
r-class 7.3_14 r3.2.2_0a defaults
r-cluster 2.0.3 r3.2.2_0a defaults
r-codetools 0.2_14 r3.2.2_0a defaults
r-foreign 0.8_66 r3.2.2_0a defaults
r-gdata 2.17.0 r3.2.2_0a defaults
r-gplots 2.17.0 r3.2.2_0a defaults
r-gtools 3.5.0 r3.2.2_0a defaults
r-kernsmooth 2.23_15 r3.2.2_0a defaults
r-lattice 0.20_33 r3.2.2_0a defaults
r-mass 7.3_45 r3.2.2_0a defaults
r-matrix 1.2_2 r3.2.2_0a defaults
r-mgcv 1.8_9 r3.2.2_0a defaults
r-nlme 3.1_122 r3.2.2_0a defaults
r-nnet 7.3_11 r3.2.2_0a defaults
r-recommended 3.2.2 r3.2.2_0 defaults
r-rpart 4.1_10 r3.2.2_0a defaults
r-spatial 7.3_11 r3.2.2_0a defaults
r-survival 2.38_3 r3.2.2_0a defaults
readline 7.0 hf8c457e_1001 conda-forge
reportlab 3.5.12 py27hbd3ef63_1000 conda-forge
samtools 1.9 h91753b0_5 bioconda
scikit-learn 0.20.1 py27h4989274_0 defaults
scipy 1.1.0 py27hd20e5f9_0 defaults
setuptools 40.8.0 py27_0 conda-forge
singledispatch 3.4.0.3 py27_1000 conda-forge
sip 4.18.1 py27hf484d3e_1000 conda-forge
six 1.12.0 py27_1000 conda-forge
spades 3.13.0 0 bioconda
sqlite 3.26.0 h67949de_1000 conda-forge
subprocess32 3.5.3 py27h14c3975_0 conda-forge
t_coffee 11.0.8 py27_2 bioconda
tbb 2019.3 h6bb024c_1000 conda-forge
tbl2asn 25.6 3 bioconda
tidyp 1.04 1 bioconda
tk 8.6.9 h84994c4_1000 conda-forge
tktable 2.10 h14c3975_0 defaults
tornado 5.1.1 py27h14c3975_1000 conda-forge
trimmomatic 0.39 0 bioconda
wheel 0.33.0 py27_0 conda-forge
xopen 0.5.0 py_0 bioconda
xorg-kbproto 1.0.7 h14c3975_1002 conda-forge
xorg-libice 1.0.9 h14c3975_1004 conda-forge
xorg-libsm 1.2.3 h4937e3b_1000 conda-forge
xorg-libx11 1.6.7 h14c3975_1000 conda-forge
xorg-libxau 1.0.9 h14c3975_0 conda-forge
xorg-libxdmcp 1.1.2 h14c3975_1007 conda-forge
xorg-libxext 1.3.3 h14c3975_1004 conda-forge
xorg-libxpm 3.5.12 h14c3975_1002 conda-forge
xorg-libxrender 0.9.10 h14c3975_1002 conda-forge
xorg-libxt 1.1.5 h14c3975_1002 conda-forge
xorg-renderproto 0.11.1 h14c3975_1002 conda-forge
xorg-xextproto 7.3.0 h14c3975_1002 conda-forge
xorg-xproto 7.0.31 h14c3975_1007 conda-forge
xz 5.2.4 h14c3975_1001 conda-forge
zlib 1.2.11 h14c3975_1004 conda-forge