Add post install command to FROGS dependencies

tools/FROGS_affiliation/FROGS_affiliation.yaml

@@ -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: [

tools/FROGS_cluster/FROGS_cluster.yaml

@@ -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:
       [

tools/FROGS_filter_affiliation/FROGS_filter_affiliation.yaml

@@ -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:

tools/FROGS_preprocess/FROGS_preprocess.yaml

@@ -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:  {

tools/FROGS_remove_chimera/FROGS_remove_chimera.yaml

@@ -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",