diff options
| -rwxr-xr-x | run_bnw.sh | 13 | ||||
| -rwxr-xr-x | run_genecup.sh | 7 | ||||
| -rwxr-xr-x | run_power.sh | 3 | ||||
| -rwxr-xr-x | run_singlecell.sh | 7 | ||||
| -rw-r--r-- | shepherd/init.d/genecup.scm | 2 | ||||
| -rwxr-xr-x | update_archive-pubmed.sh | 4 |
6 files changed, 25 insertions, 11 deletions
@@ -1,5 +1,16 @@ #!/bin/sh # This version for the bnw guix profile which includes guix-bioinformatics, using bnw-channels.scm. -$(/home/shepherd/guix-profiles/bnw/bin/guix system container /home/shepherd/guix-bioinformatics/gn/services/bnw-container.scm --share=/home/shepherd/logs/bnw-server=/var/log --network) +# +# Note the deployment shifted, see https://issues.genenetwork.org/issues/systems/apps + +# $(/home/shepherd/guix-profiles/bnw/bin/guix system container /home/shepherd/guix-bioinformatics/gn/services/bnw-container.scm --share=/home/shepherd/logs/bnw-server=/var/log --network) + +# Here we simply build the system container and link it: + +rm -vf /usr/local/bin/bnw-app-container + +/home/shepherd/guix-profiles/bnw/bin/guix system container /home/shepherd/guix-bioinformatics/gn/services/bnw-container.scm --share=/home/shepherd/logs/bnw-server=/var/log --network --root=/usr/local/bin/bnw-app-container + +/usr/local/bin/bnw-app-container #$(/home/shepherd/guix-profiles/bnw/bin/guix system container -L /home/shepherd/guix-past/modules -L /home/shepherd/guix-bioinformatics /home/shepherd/guix-bioinformatics/gn/services/bnw-container.scm --share=/home/shepherd/logs/bnw-server=/var/log --network) diff --git a/run_genecup.sh b/run_genecup.sh index ea43a0d..1e79e85 100755 --- a/run_genecup.sh +++ b/run_genecup.sh @@ -1,9 +1,8 @@ #!/bin/sh -export EDIRECT_PUBMED_MASTER=/export2/PubMed -export PERL_LWP_SSL_CA_FILE=/etc/ssl/certs/ca-certificates.crt +export EDIRECT_PUBMED_MASTER=/export3/PubMed export TMPDIR=/export/ratspub/tmp -export NLTK_DATA=/export2/PubMed/nltk_data +export NLTK_DATA=/export3/PubMed/nltk_data # This version for the genecup guix profile which includes guix-bioinformatics, using genecup-channels.scm. # shepherd@tux02:~/services/genecup$ ./guix/bin/guix build -L ~/services/genecup/guix-past/modules -L ~/services/genecup/guix-bioinformatics genecup-latest-with-tensorflow-native -c 24 -M 8 @@ -11,5 +10,5 @@ export NLTK_DATA=/export2/PubMed/nltk_data cd /home/shepherd/services/genecup cd $(/home/shepherd/services/genecup/guix/bin/guix build -L /home/shepherd/services/genecup/guix-past/modules -L /home/shepherd/services/genecup/guix-bioinformatics genecup-latest-with-tensorflow-native -c 4) -/home/shepherd/services/genecup/guix/bin/guix shell -L /home/shepherd/services/genecup/guix-past/modules -L /home/shepherd/services/genecup/guix-bioinformatics genecup-latest-with-tensorflow-native -- ./server.py +/home/shepherd/services/genecup/guix/bin/guix shell --root=/home/shepherd/guix-profiles/genecup-app -C -N --expose=/etc/ssl/certs --expose=$EDIRECT_PUBMED_MASTER --share=$TMPDIR -L /home/shepherd/services/genecup/guix-past/modules -L /home/shepherd/services/genecup/guix-bioinformatics genecup-latest-with-tensorflow-native coreutils-minimal -- env TMPDIR=$TMPDIR EDIRECT_PUBMED_MASTER=$EDIRECT_PUBMED_MASTER NLTK_DATA=$NLTK_DATA ./server.py diff --git a/run_power.sh b/run_power.sh index 378896f..851bacb 100755 --- a/run_power.sh +++ b/run_power.sh @@ -1,2 +1,3 @@ #!/bin/sh -/home/shepherd/guix-profiles/power/bin/guix environment --ad-hoc bxd-power-calculator-app -- sh -c 'R_LIBS_USER=$GUIX_ENVIRONMENT/site-library/ bxd-power-calculator-app' + +/home/wrk/opt/guix-pull-5-link/bin/guix shell --root=/home/shepherd/guix-profiles/bxd-power-app bxd-power-calculator-app -- sh -c 'R_LIBS_USER=$GUIX_ENVIRONMENT/site-library/ bxd-power-calculator-app' diff --git a/run_singlecell.sh b/run_singlecell.sh index 3c615b8..5ca8f78 100755 --- a/run_singlecell.sh +++ b/run_singlecell.sh @@ -1,3 +1,6 @@ #!/bin/sh -/home/shepherd/guix-profiles/singlecell/bin/guix download https://bioconductor.org/packages/3.11/bioc/src/contrib/multtest_2.44.0.tar.gz -/home/shepherd/guix-profiles/singlecell/bin/guix environment --ad-hoc singlecellrshiny -- sh -c 'R_LIBS_USER=$GUIX_ENVIRONMENT/site-library/ singlecellrshiny' +# /home/shepherd/guix-profiles/singlecell/bin/guix download https://bioconductor.org/packages/3.11/bioc/src/contrib/multtest_2.44.0.tar.gz +# /home/shepherd/guix-profiles/singlecell/bin/guix environment --ad-hoc singlecellrshiny -- sh -c 'R_LIBS_USER=$GUIX_ENVIRONMENT/site-library/ singlecellrshiny' + +/home/wrk/opt/guix-pull-5-link/bin/guix shell --root=? singlecellrshiny -- sh -c 'R_LIBS_USER=$GUIX_ENVIRONMENT/site-library/ singlecellrshiny' + diff --git a/shepherd/init.d/genecup.scm b/shepherd/init.d/genecup.scm index 36b6145..99ebe75 100644 --- a/shepherd/init.d/genecup.scm +++ b/shepherd/init.d/genecup.scm @@ -5,7 +5,7 @@ #:start (make-forkexec-constructor '("/home/shepherd/run_genecup.sh") #:environment-variables - (list "EDIRECT_PUBMED_MASTER=/export2/PubMed" + (list "EDIRECT_PUBMED_MASTER=/export3/PubMed" "NLTK_DATA=/home/hchen/nltk_data" "PERL_LWP_SSL_CA_FILE=/etc/ssl/certs/ca-certificates.crt" "TMPDIR=/export/ratspub/tmp") diff --git a/update_archive-pubmed.sh b/update_archive-pubmed.sh index c242953..ce210b7 100755 --- a/update_archive-pubmed.sh +++ b/update_archive-pubmed.sh @@ -1,6 +1,6 @@ #!/bin/sh -export EDIRECT_PUBMED_MASTER=/export2/PubMed +export EDIRECT_PUBMED_MASTER=/export3/PubMed export PERL_LWP_SSL_CA_FILE=/etc/ssl/certs/ca-certificates.crt -export NLTK_DATA=/export2/PubMed/nltk_data +export NLTK_DATA=/export3/PubMed/nltk_data unset PATH $(/home/shepherd/guix-profiles/genecup/bin/guix build edirect)/bin/archive-pubmed |