[med-svn] r23637 - trunk/community/edam
Steffen Möller
moeller at moszumanska.debian.org
Wed Jan 18 10:39:38 UTC 2017
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
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