Commit 0333b91e authored by khalid's avatar khalid
Browse files

Add post install command to FROGS dependencies

parent f226e01c
......@@ -89,24 +89,20 @@
"apt-get install python3-scipy" # demande confirmation
],
ncbi-blast-2.10.1: [
"cd /opt/biotools/FROGS-3.2.3/bin",
"cd /opt/biotools/",
"wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.10.1/ncbi-blast-2.10.1+-x64-linux.tar.gz",
"tar xvzf ncbi-blast-2.10.1+-x64-linux.tar.gz",
# add to FROGS
"ln -s /opt/biotools/FROGS-3.2.3/bin/ncbi-blast-2.10.1+/bin/blastn /opt/biotools/FROGS-3.2.3/libexec/."
],
Needleall 6.6.0.0: [
# requires pdf and png support
"apt-get install -y libhpdf-dev libpng-dev",
"cd /opt/biotools/FROGS-3.2.3/bin",
"cd /opt/biotools/",
"wget ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.6.0.tar.gz",
"tar xvf EMBOSS-6.6.0.tar.gz",
"cd EMBOSS-6.6.0",
"./configure --prefix=/opt/biotools/FROGS-3.2.3/bin/EMBOSS-6.6.0",
"./configure --prefix=/opt/biotools/EMBOSS-6.6.0",
"make",
"make install",
# add to FROGS
"ln -s /opt/biotools/FROGS-3.2.3/bin/EMBOSS-6.6.0/emboss/needleall /opt/biotools/FROGS-3.2.3/libexec/."
"make install",
],
ant : ["apt-get install ant"],
RDPclasifier: [
......@@ -117,8 +113,16 @@
"git submodule init",
"git submodule update",
"make",
# add to FROGS
"ln -s opt/biotools/RDPTools/classifier.jar /opt/biotools/FROGS-3.2.3/libexec/."
],
frogs_post_install: [
# add blast to FROGS
"ln -s /opt/biotools/ncbi-blast-2.10.1+/bin/blastn /opt/biotools/FROGS-3.2.3/libexec/.",
# add RDP to FROGS
"ln -s opt/biotools/RDPTools/classifier.jar /opt/biotools/FROGS-3.2.3/libexec/.",
# add needleall to FROGS
"ln -s /opt/biotools/EMBOSS-6.6.0/emboss/needleall /opt/biotools/FROGS-3.2.3/libexec/."
],
},
data: [
......
......@@ -69,13 +69,15 @@
"apt-get install python3-scipy" # demande confirmation
],
swarm 3.0.O: [
"cd /opt/biotools/FROGS-3.2.3/bin",
"cd /opt/biotools/",
"wget https://github.com/torognes/swarm/archive/v3.0.0.tar.gz",
"tar -vxzf v3.0.0.tar.gz",
"cd swarm-3.0.0/src",
"make",
"cd ..",
" ln -s /opt/biotools/FROGS-3.2.3/bin/swarm-3.0.0/bin/swarm /opt/biotools/FROGS-3.2.3/."
],
frog_swarm: [
" ln -s /opt/biotools/swarm-3.0.0/bin/swarm /opt/biotools/FROGS-3.2.3/."
],
mbb_mqc_plugin:
[
......
......@@ -122,7 +122,9 @@
"cd /opt/biotools/",
"wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.10.1/ncbi-blast-2.10.1+-x64-linux.tar.gz",
"tar xvzf ncbi-blast-2.10.1+-x64-linux.tar.gz",
# add to FROGS
],
frogs_blast_post_install: [
# add blast to FROGS
"ln -s /opt/biotools/ncbi-blast-2.10.1+/bin/blastn /opt/biotools/FROGS-3.2.3/libexec/."
],
mbb_mqc_plugin:
......
......@@ -210,7 +210,7 @@
],
vsearch 2.17.0: [
"apt-get install autoconf libz-dev libbz2-dev", # deja installé
"cd /opt/biotools/FROGS-3.2.3/bin",
"cd /opt/biotools/",
"wget https://github.com/torognes/vsearch/archive/v2.17.0.tar.gz",
"tar xzf v2.17.0.tar.gz",
"cd vsearch-2.17.0",
......@@ -221,13 +221,15 @@
],
cutadapt 2.10: [
"apt-get install python3-pip", # deja present
"cd /opt/biotools/FROGS-3.2.3/bin",
"cd /opt/biotools/",
"mkdir cutadapt-2.10",
"cd cutadapt-2.10",
"pip3 install --prefix=/opt/biotools/FROGS-3.2.3/bin/cutadapt-2.10 cutadapt==2.10",
"echo 'export PYTHONPATH=/opt/biotools/FROGS-3.2.3/bin/cutadapt-2.10/lib/python3.8/site-packages:$PYTHONPATH' >> /etc/environment",
# add to FROGS
"ln -s /opt/biotools/FROGS-3.2.3/bin/cutadapt-2.10/bin/cutadapt /opt/biotools/FROGS-3.2.3/libexec/."
"pip3 install --prefix=/opt/biotools/cutadapt-2.10 cutadapt==2.10",
"echo 'export PYTHONPATH=/opt/biotools/cutadapt-2.10/lib/python3.8/site-packages:$PYTHONPATH' >> /etc/environment",
],
frogs_cutadapt: [
# add to FROGS
"ln -s /opt/biotools/cutadapt-2.10/bin/cutadapt /opt/biotools/FROGS-3.2.3/libexec/."
],
},
citations: {
......
......@@ -58,7 +58,7 @@
],
vsearch 2.17.0: [
"apt-get install autoconf libz-dev libbz2-dev", # deja installé
"cd /opt/biotools/FROGS-3.2.3/bin",
"cd /opt/biotools/",
"wget https://github.com/torognes/vsearch/archive/v2.17.0.tar.gz",
"tar xzf v2.17.0.tar.gz",
"cd vsearch-2.17.0",
......
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