Author: moeller Date: 2017-01-18 10:39:37 +0000 (Wed, 18 Jan 2017) New Revision: 23637
Added: trunk/community/edam/packages.list.txt trunk/community/edam/packages.list.update.sh Modified: trunk/community/edam/registry-tool-iterator.sh Log: Retrieval of packages list, improved iteration Added: trunk/community/edam/packages.list.txt =================================================================== --- trunk/community/edam/packages.list.txt (rev 0) +++ trunk/community/edam/packages.list.txt 2017-01-18 10:39:37 UTC (rev 23637) @@ -0,0 +1,65 @@ +acedb +adun.app +aevol +altree +autodocksuite +autodock-vina +ball +berkeley-express +blimps +cassiopee +coils +cufflinks +dialign-t +dindel +discosnp +dnaclust +dssp +edtsurf +epcr +fermi-lite +freecontact +ghemical +htslib +hyphy +jellyfish +kmer +libfastahack +libncl +libsmithwaterman +libssw +libvcflib +logol +maffilter +mapsembler2 +microbiomeutil +minia +mira +mrbayes +murasaki +nanopolish +ncbi-blast+ +ncbi-tools6 +openms +paraclu +pbsuite +perm +prime-phylo +profnet +progressivemauve +python-cutadapt +python-dendropy +ray +r-cran-genabel +relion +r-other-mott-happy +salmon +seqan2 +sra-sdk +staden-io-lib +swarm-cluster +tophat +tree-puzzle +tvc +velvet +zalign Added: trunk/community/edam/packages.list.update.sh =================================================================== --- trunk/community/edam/packages.list.update.sh (rev 0) +++ trunk/community/edam/packages.list.update.sh 2017-01-18 10:39:37 UTC (rev 23637) @@ -0,0 +1,25 @@ +#!/bin/bash +set -e +dest="$(dirname $0)/packages.list.txt" + +echo "Writing packages list to '$dest'" +( +wget -O - https://anonscm.debian.org/cgit/blends/projects/med.git/plain/tasks/bio | grep Depends | cut -f2 -d: | tr ", " "\n" | tr -d "|" | sort -u | while + read packagename +do + a=$(apt-cache show $packagename | head -n 2) + p="" + q="" + if echo $a|grep -q "Source: "; then + q=$(echo $a | sed -e '/^.*Source:/s/^.*Source: *//' -e 's/ *Version:.*//' -e 's/ *(.*) *//') + echo $q + else + p=$(echo $a | sed -e '/Package/s/^Package: *//' -e 's/ *Version:.*//') + echo $q + fi + # for debugging + #echo "p='$p'" + #echo "q='$q'" + #echo +done +) | grep -v "^E:" | sort -u | egrep -v "^ *$"> $dest Property changes on: trunk/community/edam/packages.list.update.sh ___________________________________________________________________ Added: svn:executable + * Modified: trunk/community/edam/registry-tool-iterator.sh =================================================================== --- trunk/community/edam/registry-tool-iterator.sh 2017-01-18 10:23:22 UTC (rev 23636) +++ trunk/community/edam/registry-tool-iterator.sh 2017-01-18 10:39:37 UTC (rev 23637) @@ -6,8 +6,13 @@ fi DONTUPDATE=true +#DONTUPDATE=false + DONTOVERWRITE=true + +# Set to true if no new repositories shall be downloaded DONTCLONE=true +#DONTCLONE=false TOOLDIR=$(realpath $(dirname $0)) @@ -46,58 +51,83 @@ exit 1 fi -if ! $DONTCLONE; then - #for p in $EDAMPACKAGESINGIT - cat "$TOOLDIR/packages.list.txt" | while read p - 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/$p.json'" - continue - fi +echo +echo "I: *** Retrieving package source tree from Debian Med git repository ***" +echo - origin="https://anonscm.debian.org/git/debian-med/$p.git"; - #origin="ssh://anonscm.debian.org/git/debian-med/$p.git" - if [ -d "$GITDIR"/"$p" ]; then - if $DONTUPDATE; then - echo " is existing, will not check for any later version" - else - echo " is existing, will pull latest version from Debian Med git repository '$origin'" - cd "$GITDIR"/"$p" - if ! git pull; then - echo - echo "E: Could not pull latest revision for '$p' from $origin - skipped" - continue - fi +#for p in $EDAMPACKAGESINGIT +cat "$TOOLDIR/packages.list.txt" | while read p +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 + if $DONTUPDATE; then + echo " is existing, will not check for any later version" + else + echo " is existing, will pull latest version from Debian Med git repository '$origin'" + cd "$GITDIR"/"$p" + if ! git pull; then + echo + echo "W: Could not pull latest revision for '$p' from $origin - skipped, git status shown below" + git status + continue fi + if ! git gc; then + echo + echo "E: Could not garbage-collect package '$p' - fix this" + exit 1 + fi + fi + else + echo -n " is not existing " + if $DONTCLONE; then + echo " [skipped]" + continue else - echo " is not existing, will clone from Debian Med git repository '$origin'" + echo -n ", will clone from Debian Med git repository '$origin'" if ! git clone --quiet --branch=master --single-branch $origin; then echo echo "E: Could not clone package '$p' from $origin - skipped" continue fi + cd $p + if ! git gc; then + echo + echo "E: Could not garbage-collect freshly cloned package '$p' - fix this" + exit 1 + fi fi + fi - cd "$GITDIR"/"$p" - git checkout master + cd "$GITDIR"/"$p" + git checkout master - if [ ! -r debian/upstream/edam ]; then - echo "W: The package '$p' suprisingly does not feature an EDAM annotation file" - continue - fi + if [ ! -r debian/upstream/edam ]; then + echo "W: The package '$p' suprisingly does not feature an EDAM annotation file" + continue + fi - if ! yamllint debian/upstream/edam; then - echo - echo "E: The package '$p' has a problem with its EDAM annotation. Please fix." - exit 1 - fi - done -fi + if ! yamllint debian/upstream/edam; then + echo + echo "E: The package '$p' has a syntactic problem with its EDAM annotation. Please fix." + exit 1 + fi +done +echo +echo "I: *** Repository of Debian Med packages is in shape, now transcribing for bio.tools ***" +echo + #for p in $EDAMPACKAGESINGIT cat "$TOOLDIR/packages.list.txt" | grep -v ^# | while read p do _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
