[med-svn] r23641 - trunk/community/edam

Wed Jan 18 16:34:54 UTC 2017

Author: moeller
Date: 2017-01-18 16:34:53 +0000 (Wed, 18 Jan 2017)
New Revision: 23641

Modified:
   trunk/community/edam/packages.list.txt
   trunk/community/edam/registry-tool-iterator.sh
   trunk/community/edam/registry-tool.py
Log:
Increased flexibility for remote machine

Modified: trunk/community/edam/packages.list.txt
===================================================================

--- trunk/community/edam/packages.list.txt	2017-01-18 11:19:44 UTC (rev 23640)
+++ trunk/community/edam/packages.list.txt	2017-01-18 16:34:53 UTC (rev 23641)
@@ -1,65 +1,305 @@
+abacas
+abyss
 acedb
-adun.app
+adapterremoval
 aevol
+alien-hunter
+alter-sequence-alignment
 altree
+amap-align
+ampliconnoise
+anfo
+aragorn
+arb
+arden
+art-nextgen-simulation-tools
+artemis
+artfastqgenerator
+autodock-vina
 autodocksuite
-autodock-vina
+autodocktools
 ball
-berkeley-express
+bamtools
+barrnap
+bcftools
+beast-mcmc
+bedtools
+blasr
 blimps
+bowtie
+bowtie2
+boxshade
+brig
+bwa
 cassiopee
+cd-hit
+cdbfasta
+cgview
+circlator
+circos
+clearcut
+clonalframe
+clustalo
+clustalw
+clustalx
+cluster3
 coils
+concavity
+conservation-code
 cufflinks
+daligner
+dascrubber
+dazzdb
+dialign
 dialign-t
-dindel
 discosnp
+disulfinder
 dnaclust
 dssp
+ea-utils
 edtsurf
+eigensoft
+embassy-domainatrix
+embassy-domalign
+embassy-domsearch
+embassy-phylip
+emboss
 epcr
-fermi-lite
+exonerate
+falcon
+fastaq
+fastdnaml
+fastlink
+fastml
+fastqc
+fasttree
+fastx-toolkit
+ffindex
+figtree
+filo
+fitgcp
+flexbar
 freecontact
-ghemical
+fsm-lite
+gamgi
+garlic
+gasic
+gbrowse
+gdpc
+genometools
+gentle
+gff2aplot
+gff2ps
+giira
+glam2
+gmap
+graphlan
+grinder
+gromacs
+gubbins
+harvest-tools
+hhsuite
+hilive
+hmmer
+hmmer2
 htslib
 hyphy
+idba
+igv
+infernal
+ipig
+iqtree
+jaligner
+jalview
 jellyfish
+jmodeltest
+jmol
+kalign
+kineticstools
+kissplice
 kmer
+kraken
+last-align
+lefse
 libfastahack
-libncl
+librg-utils-perl
 libsmithwaterman
 libssw
 libvcflib
 logol
+loki
+ltrsift
+macs
 maffilter
+mafft
+mapdamage
 mapsembler2
+maq
+maqview
+massxpert
+mauve-aligner
+melting
+metaphlan2
+metastudent
+mgltools-cadd
+mgltools-pmv
+mgltools-vision
+mhap
+microbegps
 microbiomeutil
 minia
+mipe
 mira
+mlv-smile
+mothur
 mrbayes
+mummer
 murasaki
+muscle
+mustang
 nanopolish
 ncbi-blast+
+ncbi-seg
 ncbi-tools6
+neobio
+njplot
+norsnet
+norsp
 openms
+paml
 paraclu
+parsinsert
+parsnp
+pbalign
+pbbarcode
+pbdagcon
+pbgenomicconsensus
+pbh5tools
 pbsuite
+pdb2pqr
+perlprimer
 perm
+phipack
+phylip
+phyml
+phyutility
+picard-tools
+placnet
+plasmidomics
+plast
+plink
+plink1.9
+poa
+populations
+poretools
+prank
+predictnls
+predictprotein
 prime-phylo
+primer3
+proalign
+probabel
+probalign
+probcons
+proda
+prodigal
+profbval
+profisis
 profnet
+profphd
+profphd-utils
+proftmb
 progressivemauve
+proteinortho
+prottest
+pycorrfit
+pymol
+pynast
+pyscanfcs
+python-cogent
 python-cutadapt
 python-dendropy
+qiime
+r-bioc-biostrings
+r-bioc-cummerbund
+r-bioc-edger
+r-bioc-gviz
+r-bioc-hilbertvis
+r-bioc-limma
+r-bioc-rtracklayer
+r-cran-adegenet
+r-cran-adephylo
+r-cran-ape
+r-cran-distory
+r-cran-genabel
+r-cran-phangorn
+r-cran-qtl
+r-cran-seqinr
+r-cran-treescape
+r-cran-vegan
+r-other-mott-happy
+raccoon
+rasmol
+raster3d
+rate4site
+raxml
 ray
-r-cran-genabel
+readseq
 relion
-r-other-mott-happy
-salmon
-seqan2
+repeatmasker-recon
+reprof
+rna-star
+rnahybrid
+roary
+rtax
+saint
+samtools
+seaview
+seer
+seq-gen
+seqan
+seqtk
+sga
+sibsim4
+sickle
+sift
+sigma-align
+sim4
+smalt
+#smrtanalysis
+snap
+sniffles
+snp-sites
+soapdenovo
+soapdenovo2
+spades
+sprai
+spread-phy
+squizz
 sra-sdk
+ssake
+stacks
+staden
 staden-io-lib
-swarm-cluster
+subread
+surankco
+t-coffee
+tantan
+theseus
+tigr-glimmer
+tm-align
 tophat
+transtermhp
 tree-puzzle
-tvc
+treeview
+treeviewx
+trimmomatic
+uc-echo
+ugene
+varscan
+vcftools
 velvet
+velvetoptimiser
+vsearch
+wise
 zalign

Modified: trunk/community/edam/registry-tool-iterator.sh
===================================================================
--- trunk/community/edam/registry-tool-iterator.sh	2017-01-18 11:19:44 UTC (rev 23640)
+++ trunk/community/edam/registry-tool-iterator.sh	2017-01-18 16:34:53 UTC (rev 23641)
@@ -5,6 +5,11 @@
 	exit 1
 fi
 
+if [ ! -x /usr/bin/yamllint ]; then
+	echo "E: Please install yamllint"
+	exit 1
+fi
+
 DONTUPDATE=true
 #DONTUPDATE=false
 
@@ -22,15 +27,14 @@
 
 # And also:
 # filo 
-GITDIR=/home/moeller/git/debian-med
+GITDIR=$HOME/git/debian-med
 
-JSONBUFFERDIR=/home/moeller/git/json-buffer
+JSONBUFFERDIR=$HOME/git/json-buffer
 JSONBUFFERSUBDIR=records
 
 if [ ! -r EDAM.owl ]; then
 	echo "I: Retrieving current version of EDAM ontology"
 	wget http://www.edamontology.org/EDAM.owl
-	exit
 fi
 edamversion=$(grep doap:Version EDAM.owl | cut -f2 -d\> | cut -f1 -d\<)
 echo "I: Comparing terms against EDAM version '$edamversion'"
@@ -42,7 +46,9 @@
 fi
 
 if [ ! -d "$JSONBUFFERDIR" ]; then
-	echo "E: The diretory destined to hold the generated records is not existing. $JSONBUFFERDIR'" 
+	echo "E: The directory destined to hold the generated records is not existing."
+	echo "   Please consider running "
+        echo "      git clone https://github.com/bio-tools-community/json-buffer '$JSONBUFFERDIR'" 
 	exit -1
 fi
 
@@ -70,12 +76,6 @@
 do
 	cd "$GITDIR"  # We may have moved into a subdir
 	echo -n "I: Preparing package '$p'"
-
-	if $DONTOVERWRITE && [ -r "$JSONBUFFERDIR"/"$JSONBUFFERSUBDIR"/"$p".json ] ; then
-		echo " not overwriting exiting '$JSONBUFFERDIR/$JSONBUFFERSUBDIR/$p.json'"
-		continue
-	fi
-
 	origin="https://anonscm.debian.org/git/debian-med/$p.git"
 	#origin="ssh://anonscm.debian.org/git/debian-med/$p.git"
 	if [ -d "$GITDIR"/"$p" ]; then
@@ -140,6 +140,14 @@
 #for p in $EDAMPACKAGESINGIT
 cat "$TOOLDIR/packages.list.txt" | grep -v ^# | while read p
 do
+
+	dest="$JSONBUFFERDIR"/"$JSONBUFFERSUBDIR"/"$p".json
+
+	if $DONTOVERWRITE && [ -r "$dest" ] ; then
+		echo " not overwriting exiting '$dest'"
+		continue
+	fi
+
 	echo -n "I: Package '$p'"
 	if [ ! -d "$GITDIR"/"$p" ]; then
 		echo " not existing in '$GITDIR/$p' - skipped"
@@ -150,8 +158,7 @@
 		continue
 	fi
 
-	dest="$JSONBUFFERDIR"/"$JSONBUFFERSUBDIR"/"$p".json
-	echo -n " creating $dest"
+	echo -n " writing to $dest"
 	cd "$GITDIR"/"$p"
 	#git checkout master
 	python "$TOOLDIR"/registry-tool.py "$GITDIR"/"$p" > $dest

Modified: trunk/community/edam/registry-tool.py
===================================================================
--- trunk/community/edam/registry-tool.py	2017-01-18 11:19:44 UTC (rev 23640)
+++ trunk/community/edam/registry-tool.py	2017-01-18 16:34:53 UTC (rev 23641)
@@ -19,7 +19,8 @@
 
 #EDAM_DOC = doc = etree.parse("/home/hmenager/edamontology/EDAM_1.13_dev.owl")
 #EDAM_DOC = doc = etree.parse("EDAM.owl")
-doc = etree.parse("/home/moeller/debian-med/community/edam/EDAM.owl")
+#doc = etree.parse("/home/moeller/debian-med/community/edam/EDAM.owl")
+doc = etree.parse("/home/kalas/edam/EDAM.owl")
 EDAM_DOC = doc.getroot()
 
 def check_id(label, axis):


