[med-svn] r9440 - in trunk/packages/ensembl/ensembl/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Thu Jan 26 19:21:23 UTC 2012
Author: tille
Date: 2012-01-26 19:21:23 +0000 (Thu, 26 Jan 2012)
New Revision: 9440
Added:
trunk/packages/ensembl/ensembl/trunk/debian/patches/get_rid_of_ksh.patch
Modified:
trunk/packages/ensembl/ensembl/trunk/debian/changelog
trunk/packages/ensembl/ensembl/trunk/debian/control
trunk/packages/ensembl/ensembl/trunk/debian/patches/series
Log:
Commit current state of changes to Ensembl after traveling to Debian Med sprint
Modified: trunk/packages/ensembl/ensembl/trunk/debian/changelog
===================================================================
--- trunk/packages/ensembl/ensembl/trunk/debian/changelog 2012-01-26 19:20:25 UTC (rev 9439)
+++ trunk/packages/ensembl/ensembl/trunk/debian/changelog 2012-01-26 19:21:23 UTC (rev 9440)
@@ -67,8 +67,10 @@
to advertise csh for no need at all and the patch is just dropping
csh references.
* debian/init.d: Added description
+ * debian/patches/get_rid_of_ksh.patch: Replace ksh code by POSIX
+ shell
- -- Andreas Tille <tille at debian.org> Thu, 15 Dec 2011 19:01:29 +0100
+ -- Andreas Tille <tille at debian.org> Wed, 28 Dec 2011 19:20:54 +0100
ensembl (63-1~lucid1) lucid; urgency=low
Modified: trunk/packages/ensembl/ensembl/trunk/debian/control
===================================================================
--- trunk/packages/ensembl/ensembl/trunk/debian/control 2012-01-26 19:20:25 UTC (rev 9439)
+++ trunk/packages/ensembl/ensembl/trunk/debian/control 2012-01-26 19:21:23 UTC (rev 9440)
@@ -77,7 +77,7 @@
Package: libensembl-core-perl
Architecture: all
-Depends: ${misc:Depends}, ksh | mksh | pdksh | zsh, bioperl1.2.3 | bioperl
+Depends: ${misc:Depends}, bioperl1.2.3 | bioperl
Suggests: tk
Section: non-free/perl
Description: core libraries of Ensembl API
Added: trunk/packages/ensembl/ensembl/trunk/debian/patches/get_rid_of_ksh.patch
===================================================================
--- trunk/packages/ensembl/ensembl/trunk/debian/patches/get_rid_of_ksh.patch (rev 0)
+++ trunk/packages/ensembl/ensembl/trunk/debian/patches/get_rid_of_ksh.patch 2012-01-26 19:21:23 UTC (rev 9440)
@@ -0,0 +1,228 @@
+Author: Andreas Tille <tille at debian.org>
+Date: Wed, 28 Dec 2011 19:20:54 +0100
+Description: Get rid of ksh code and replace it by POSIX
+ Because ksh and its clones are forcing extra dependencies
+ for no pratical use (rather forcing users to install extra packages
+ we hereby get rid of the ksh specific code
+
+--- ensembl-65.orig/ensembl/misc-scripts/ontology/scripts/get_OBO_files.ksh
++++ ensembl-65/ensembl/misc-scripts/ontology/scripts/get_OBO_files.ksh
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+
+ # GO - Gene Ontology
+ wget -O GO.obo "http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo"
+--- ensembl-65.orig/ensembl/misc-scripts/id_mapping/utils/myManager.ksh
++++ ensembl-65/ensembl/misc-scripts/id_mapping/utils/myManager.ksh
+@@ -1,8 +1,8 @@
+-#!/bin/ksh
++#!/bin/sh
+
+ scriptname=$0
+
+-function usage {
++usage () {
+ cat <<EOT
+
+ Usage:
+@@ -13,8 +13,8 @@
+ }
+
+ if [[ ! -e ./manage_id_mapping_tables.pl ]]; then
+- print -u2 "Expected to find the following executable file here:"
+- print -u2 "\tmanage_id_mapping_tables.pl"
++ echo "Expected to find the following executable file here:"
++ echo " manage_id_mapping_tables.pl"
+ exit
+ fi
+
+--- ensembl-65.orig/ensembl/misc-scripts/id_mapping/myRun.ksh
++++ ensembl-65/ensembl/misc-scripts/id_mapping/myRun.ksh
+@@ -1,8 +1,8 @@
+-#!/bin/ksh
++#!/bin/sh
+
+ scriptname=$0
+
+-function usage {
++usage () {
+ cat >&2 <<EOT
+
+ Usage:
+@@ -22,8 +22,8 @@
+ }
+
+ if [[ ! -e ./run.pl ]]; then
+- print -u2 "Expected to find the following executable file here:"
+- print -u2 "\trun.pl"
++ echo "Expected to find the following executable file here:"
++ echo " run.pl"
+ exit
+ fi
+
+@@ -37,18 +37,18 @@
+ esac
+ done
+
+-if [[ -z ${conf} || -z ${mode} ]]; then
++if [ -z ${conf} || -z ${mode} ]; then
+ usage
+ exit
+ fi
+
+-if [[ ! -f ${conf} ]]; then
+- print -u2 "The file '${conf}' does not exist."
++if [ ! -f ${conf} ]; then
++ echo "The file '${conf}' does not exist."
+ exit
+ fi
+
+-if [[ ${conf#/} == ${conf} ]]; then
+- print -u2 "The path '${conf}' is not absolute."
++if [ ${conf#/} == ${conf} ]; then
++ echo "The path '${conf}' is not absolute."
+ exit
+ fi
+
+--- ensembl-65.orig/ensembl/misc-scripts/production_database/sql/data/dump_production_database.ksh
++++ ensembl-65/ensembl/misc-scripts/production_database/sql/data/dump_production_database.ksh
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+
+ dbhost="ens-staging1"
+ dbuser="ensro"
+--- ensembl-65.orig/ensembl/misc-scripts/density_feature/DensityCalc.sh
++++ ensembl-65/ensembl/misc-scripts/density_feature/DensityCalc.sh
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+
+ # This script submits jobs to the farm to calculate the various density
+ # features for a particular core database.
+@@ -28,29 +28,29 @@
+ esac
+ done
+
+-if [[ -z ${host} || -z ${port} || -z ${dbname} || -z ${species} || -z ${user} || -z ${pass} ]]
++if [ -z ${host} -o -z ${port} -o -z ${dbname} -o -z ${species} -o -z ${user} -o -z ${pass} ]
+ then
+- print -u2 "Usage:\n\t$0 -h host -P port -d database -s species -u user -p password"
++ echo "Usage: $0 -h host -P port -d database -s species -u user -p password"
+ exit 1
+ fi
+
+ # Enter an output dir so results don't get written in the same place as your script
+-if [[ -z ${outdir} || ! -d ${outdir} ]]
++if [ -z ${outdir} -o ! -d ${outdir} ]
+ then
+ outdir=$PWD
+ fi
+
+-print "Output dir is '${outdir}'"
++echo "Output dir is '${outdir}'"
+
+ # Make sure this is a core database.
+-if [[ -n ${dbname##*_core_*} ]]; then
+- print -u2 "The database '${dbname}' is not a core database"
++if [ -n ${dbname##*_core_*} ]; then
++ echo "The database '${dbname}' is not a core database"
+ exit 1
+ fi
+
+-print "Submitting percent GC calculation to queue 'normal'"
+-print "\tThe output from this job goes to the file"
+-print "\t'${dbname}_gc.out'"
++echo "Submitting percent GC calculation to queue 'normal'"
++echo " The output from this job goes to the file"
++echo " '${dbname}_gc.out'"
+ bsub -q normal -J gc_calc \
+ -oo ${outdir}/${dbname}_gc.out \
+ -eo ${outdir}/${dbname}_gc.err \
+@@ -61,9 +61,9 @@
+ -p ${pass} \
+ -d ${dbname}
+
+-print "Submitting gene density calculation to queue 'normal'"
+-print "\tThe output from this job goes to the file"
+-print "\t'${dbname}_gene.out'"
++echo "Submitting gene density calculation to queue 'normal'"
++echo " The output from this job goes to the file"
++echo " '${dbname}_gene.out'"
+ bsub -q normal -J gene_density \
+ -oo ${outdir}/${dbname}_gene.out \
+ -eo ${outdir}/${dbname}_gene.err \
+@@ -74,9 +74,9 @@
+ -p ${pass} \
+ -d ${dbname}
+
+-print "Submitting repeat coverage calculation to queue 'long'"
+-print "\tThe output from this job goes to the file"
+-print "\t'${dbname}_repeat.out'"
++echo "Submitting repeat coverage calculation to queue 'long'"
++echo " The output from this job goes to the file"
++echo " '${dbname}_repeat.out'"
+ bsub -q long -J repeat_cov \
+ -oo ${outdir}/${dbname}_repeat.out \
+ -eo ${outdir}/${dbname}_repeat.err \
+@@ -87,9 +87,9 @@
+ -p ${pass} \
+ -d ${dbname}
+
+-print "Submitting variation density calculation to queue 'normal'"
+-print "\tThe output from this job goes to the file"
+-print "\t'${dbname}_var.out'"
++echo "Submitting variation density calculation to queue 'normal'"
++echo " The output from this job goes to the file"
++echo " '${dbname}_var.out'"
+ bsub -q normal -J var_density \
+ -oo ${outdir}/${dbname}_var.out \
+ -eo ${outdir}/${dbname}_var.err \
+@@ -100,9 +100,9 @@
+ -p ${pass} \
+ -s ${species}
+
+-print "Submitting seq region gene stats calculation to queue 'normal'"
+-print "\tThe output from this job goes to the file"
+-print "\t'${dbname}_seqreg.out'"
++echo "Submitting seq region gene stats calculation to queue 'normal'"
++echo " The output from this job goes to the file"
++echo " '${dbname}_seqreg.out'"
+ bsub -q normal -J seqreg_stats_gene \
+ -oo ${outdir}/${dbname}_seqreg_gene.out \
+ -eo ${outdir}/${dbname}_seqreg_gene.err \
+@@ -114,9 +114,9 @@
+ -d ${dbname} \
+ -s gene
+
+-print "Submitting seq region snp stats calculation to queue 'normal'"
+-print "\tThe output from this job goes to the file"
+-print "\t'${dbname}_seqreg.out'"
++echo "Submitting seq region snp stats calculation to queue 'normal'"
++echo " The output from this job goes to the file"
++echo " '${dbname}_seqreg.out'"
+ bsub -q normal -J seqreg_stats_snp \
+ -oo ${outdir}/${dbname}_seqreg_snp.out \
+ -eo ${outdir}/${dbname}_seqreg_snp.err \
+@@ -128,9 +128,9 @@
+ -d ${dbname} \
+ -s snp
+
+-print "Submitting gene_gc content calculation to queue 'normal'"
+-print "\tThe output from this job goes to the file"
+-print "\t'${dbname}_genegc.out'"
++echo "Submitting gene_gc content calculation to queue 'normal'"
++echo " The output from this job goes to the file"
++echo " '${dbname}_genegc.out'"
+ bsub -q normal -J genegc_stats \
+ -oo ${outdir}/${dbname}_genegc.out \
+ -eo ${outdir}/${dbname}_genegc.err \
+@@ -141,6 +141,6 @@
+ -p ${pass} \
+ -pattern ${dbname}
+
+-print "All jobs submitted."
++echo "All jobs submitted."
+
+ # $Id: DensityCalc.sh,v 1.9 2011-09-27 15:55:23 mk8 Exp $
Modified: trunk/packages/ensembl/ensembl/trunk/debian/patches/series
===================================================================
--- trunk/packages/ensembl/ensembl/trunk/debian/patches/series 2012-01-26 19:20:25 UTC (rev 9439)
+++ trunk/packages/ensembl/ensembl/trunk/debian/patches/series 2012-01-26 19:21:23 UTC (rev 9440)
@@ -9,3 +9,4 @@
fix_usr_bin_env_typo.patch
do_not_advertise_csh.patch
use_ksh_only_if_needed.patch
+get_rid_of_ksh.patch
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