[med-svn] r9103 - trunk/packages/ensembl/ensembl/trunk/debian/patches
Andreas Tille
tille at alioth.debian.org
Sun Dec 25 23:17:39 UTC 2011
Author: tille
Date: 2011-12-25 23:17:39 +0000 (Sun, 25 Dec 2011)
New Revision: 9103
Modified:
trunk/packages/ensembl/ensembl/trunk/debian/patches/do_not_advertise_csh.patch
Log:
Get rid of [t]csh instances inside docs and code
Modified: trunk/packages/ensembl/ensembl/trunk/debian/patches/do_not_advertise_csh.patch
===================================================================
--- trunk/packages/ensembl/ensembl/trunk/debian/patches/do_not_advertise_csh.patch 2011-12-25 23:03:07 UTC (rev 9102)
+++ trunk/packages/ensembl/ensembl/trunk/debian/patches/do_not_advertise_csh.patch 2011-12-25 23:17:39 UTC (rev 9103)
@@ -193,3 +193,225 @@
</UL>
</LI>
</OL>
+--- ensembl-65.orig/ensembl-compara/docs/healthchecks.txt
++++ ensembl-65/ensembl-compara/docs/healthchecks.txt
+@@ -5,10 +5,6 @@
+ cvs co ensj-healthcheck
+
+ set your environnement variable JAVA_HOME
+-in tcsh
+- setenv JAVA_HOME /usr/opt/java141
+-
+-or in bash
+ JAVA_HOME=/usr/opt/java141
+ export JAVA_HOME
+
+--- ensembl-65.orig/ensembl-compara/scripts/pipeline/README-homology
++++ ensembl-65/ensembl-compara/scripts/pipeline/README-homology
+@@ -119,13 +119,11 @@
+ in one's path. This can be done by either extending PATH or linking the
+ scripts to an existing directory in the PATH
+
+- tcsh$ setenv PATH ${PATH}:${BASEDIR}/ensembl-hive/scripts
+ bash$ export PATH=$PATH:$BASEDIR/ensembl-hive/scripts
+
+ You may also need to set the LSB_DEFAULTPROJECT environment variable
+ if you are using LSF across the sanger farm;
+
+- tcsh$ setenv LSB_DEFAULTPROJECT ensembl-compara
+ bash$ export LSB_DEFAULTPROJECT=ensembl-compara
+
+ There are two beekepers, one which uses LSF job submission system, and
+--- ensembl-65.orig/ensembl-compara/scripts/pipeline/README-low-coverage-genome-aligner
++++ ensembl-65/ensembl-compara/scripts/pipeline/README-low-coverage-genome-aligner
+@@ -25,11 +25,6 @@
+ cvs -d :ext:cvs.sanger.ac.uk:/nfs/ensembl/cvsroot co ensembl-hive
+ cvs -d :ext:cvs.sanger.ac.uk:/nfs/ensembl/cvsroot co ensembl-analysis
+
+-in tcsh
+- setenv BASEDIR /some/path/to/modules
+- setenv PERL5LIB ${BASEDIR}/ensembl/modules:${BASEDIR}/ensembl-pipeline/modules:${BASEDIR}/bioperl-live:${BASEDIR}/ensembl-compara:${BASEDIR}/ensembl-hive:${BASEDIR}/ensembl-analysis
+- setenv PATH $PATH:${BASEDIR}/ensembl-compara/script/pipeline:${BASEDIR}/ensembl-hive/scripts
+-
+ in bash
+ BASEDIR=/some/path/to/modules
+ PERL5LIB=${BASEDIR}/ensembl/modules:${BASEDIR}/ensembl-pipeline/modules:${BASEDIR}/bioperl-live:${BASEDIR}/ensembl-compara:${BASEDIR}/ensembl-hive:${BASEDIR}/ensembl-hive
+--- ensembl-65.orig/ensembl-compara/scripts/pipeline/README-multiplealigner
++++ ensembl-65/ensembl-compara/scripts/pipeline/README-multiplealigner
+@@ -25,11 +25,6 @@
+ cvs -d :ext:cvs.sanger.ac.uk:/nfs/ensembl/cvsroot co ensembl-hive
+ cvs -d :ext:cvs.sanger.ac.uk:/nfs/ensembl/cvsroot co ensembl-analysis
+
+-in tcsh
+- setenv BASEDIR /some/path/to/modules
+- setenv PERL5LIB ${BASEDIR}/ensembl/modules:${BASEDIR}/ensembl-pipeline/modules:${BASEDIR}/bioperl-live:${BASEDIR}/ensembl-compara:${BASEDIR}/ensembl-hive:${BASEDIR}/ensembl-analysis
+- setenv PATH $PATH:${BASEDIR}/ensembl-compara/script/pipeline:${BASEDIR}/ensembl-hive/scripts
+-
+ in bash
+ BASEDIR=/some/path/to/modules
+ PERL5LIB=${BASEDIR}/ensembl/modules:${BASEDIR}/ensembl-pipeline/modules:${BASEDIR}/bioperl-live:${BASEDIR}/ensembl-compara:${BASEDIR}/ensembl-hive:${BASEDIR}/ensembl-hive
+--- ensembl-65.orig/ensembl-compara/scripts/pipeline/README-genetree-singlelinkage
++++ ensembl-65/ensembl-compara/scripts/pipeline/README-genetree-singlelinkage
+@@ -94,16 +94,6 @@
+
+ 1.3 Perl environment
+
+-in tcsh
+- $ setenv BASEDIR /some/path/to/modules
+- $ setenv PERL5LIB ${BASEDIR}/ensembl/modules:${PERL5LIB}
+- $ setenv PERL5LIB ${BASEDIR}/ensembl-compara/modules:${PERL5LIB}
+- $ setenv PERL5LIB ${BASEDIR}/ensembl-pipeline/modules:${PERL5LIB}
+- $ setenv PERL5LIB ${BASEDIR}/ensembl-analysis/modules:${PERL5LIB}
+- $ setenv PERL5LIB ${BASEDIR}/ensembl-hive/modules:${PERL5LIB}
+- $ setenv PERL5LIB ${BASEDIR}/bioperl-live:${PERL5LIB}
+- $ setenv PERL5LIB ${BASEDIR}/bioperl-run:${PERL5LIB}
+-
+ in bash
+ $ BASEDIR=/some/path/to/modules
+ $ export PERL5LIB=${BASEDIR}/ensembl/modules:${PERL5LIB}
+@@ -276,10 +266,9 @@
+ Set the blast envirnment; these environment variables cannot be set in
+ either ::Config::Blast or ::Config::General;
+
+-in tcsh:
+- $ setenv PATH /usr/local/ensembl/bin:$PATH
+- $ setenv BLASTMAT /usr/local/ensembl/data/blastmat:$BLASTMAT
+- $ setenv BLASTFILTER /usr/local/ensembl/bin:$BLASTFILTER
++ $ export PATH=/usr/local/ensembl/bin:$PATH
++ $ export BLASTMAT=/usr/local/ensembl/data/blastmat:$BLASTMAT
++ $ export BLASTFILTER=/usr/local/ensembl/bin:$BLASTFILTER
+
+
+ 5- Create the species tree file
+@@ -489,13 +478,11 @@
+ in one's path. This can be done by either extending PATH or linking the
+ scripts to an existing directory in the PATH
+
+- tcsh$ setenv PATH ${PATH}:${BASEDIR}/ensembl-hive/scripts
+ bash$ export PATH=$PATH:$BASEDIR/ensembl-hive/scripts
+
+ You may also need to set the LSB_DEFAULTPROJECT environment variable
+ if you are using LSF across the sanger farm;
+
+- tcsh$ setenv LSB_DEFAULTPROJECT ensembl-compara
+ bash$ export LSB_DEFAULTPROJECT=ensembl-compara
+
+ There are two beekepers, one which uses LSF job submission system, and
+--- ensembl-65.orig/ensembl-compara/scripts/pipeline/README-pairaligner
++++ ensembl-65/ensembl-compara/scripts/pipeline/README-pairaligner
+@@ -46,11 +46,6 @@
+ dependancies with this code. Hopefully this should not be the case in the near future)
+ cvs -d :pserver:cvsuser at cvs.sanger.ac.uk:/cvsroot/ensembl co ensembl-pipeline
+
+-in tcsh
+- setenv BASEDIR /some/path/to/modules
+- setenv PERL5LIB ${BASEDIR}/ensembl/modules:${BASEDIR}/ensembl-pipeline/modules:${BASEDIR}/bioperl-live:${BASEDIR}/ensembl-compara:${BASEDIR}/ensembl-hive:${BASEDIR}/ensembl-analysis
+- setenv PATH $PATH:${BASEDIR}/ensembl-compara/script/pipeline:${BASEDIR}/ensembl-hive/scripts
+-
+ in bash
+ BASEDIR=/some/path/to/modules
+ PERL5LIB=${BASEDIR}/ensembl/modules:${BASEDIR}/ensembl-pipeline/modules:${BASEDIR}/bioperl-live:${BASEDIR}/ensembl-compara/modules:${BASEDIR}/ensembl-hive/modules:${BASEDIR}/ensembl-analysis/modules
+--- ensembl-65.orig/ensembl-compara/scripts/pipeline/README-chain-net
++++ ensembl-65/ensembl-compara/scripts/pipeline/README-chain-net
+@@ -7,10 +7,6 @@
+
+ cvs -d :ext:cvs.sanger.ac.uk:/nfs/ensembl/cvsroot co ensembl-analysis
+
+-in tcsh
+- setenv BASEDIR /some/path/to/modules
+- setenv PERL5LIB ${PERL5LIB}:${BASEDIR}/ensembl-analysis/modules
+-
+ in bash
+ BASEDIR=/some/path/to/modules
+ PERL5LIB=${PERL5LIB}:${BASEDIR}/ensembl-analysis/modules
+--- ensembl-65.orig/ensembl-compara/scripts/synteny/README
++++ ensembl-65/ensembl-compara/scripts/synteny/README
+@@ -34,10 +34,6 @@
+ ensembl, ensembl-compara and bioperl-live modules will be needed
+ Make sure, you've update your PERL5LIB variable to point to the modules
+
+-in tcsh
+-setenv BASEDIR /some/path/to/modules
+-setenv PERL5LIB ${BASEDIR}/bioperl-live:${BASEDIR}/ensembl/modules:${BASEDIR}/ensembl-compara/modules
+-
+ in bash
+ BASEDIR=/some/path/to/modules
+ export BASEDIR
+--- ensembl-65.orig/ensembl/misc-scripts/xref_mapping/docs/running_the_xref_pipeline.txt
++++ ensembl-65/ensembl/misc-scripts/xref_mapping/docs/running_the_xref_pipeline.txt
+@@ -93,7 +93,7 @@
+ which comes down to doing the following :-
+ Check that the LRG modules are added to perl5lib
+ so for my instance I set
+-setenv PERL5LIB ${PERL5LIB}:/nfs/users/nfs_i/ianl/LRG/code/modules
++export PERL5LIB=${PERL5LIB}:/nfs/users/nfs_i/ianl/LRG/code/modules
+
+ perl scripts/import.lrg.pl -verbose -do_all -host ens-staging -port
+ 3306 -user rw -pass password -core homo_sapiens_core_65_37
+--- ensembl-65.orig/ensembl-compara/modules/t/README
++++ ensembl-65/ensembl-compara/modules/t/README
+@@ -9,7 +9,7 @@
+
+ Example:
+
+-setenv PERL5LIB ${PERL5LIB}:${ENSHOME}/ensembl-test/modules
++export PERL5LIB=${PERL5LIB}:${ENSHOME}/ensembl-test/modules
+
+ NB: read also ensembl-test/scripts/README
+
+--- ensembl-65.orig/ensembl-variation/scripts/import/README
++++ ensembl-65/ensembl-variation/scripts/import/README
+@@ -6,10 +6,10 @@
+ Set the working directory
+
+ $ cd /some/path/to/workdir
+- $ setenv BASEDIR $PWD
++ $ export BASEDIR=$PWD
+
+ Set the path to the perl binary that is available on the cluster
+- $ setenv PERLDIR /usr/bin/perl
++ $ export PERLDIR=/usr/bin/perl
+
+ Get bioperl code
+
+@@ -33,11 +33,11 @@
+
+ Set the Perl environment
+
+- $ setenv PERL5LIB ${BASEDIR}/bioperl-live:${PERL5LIB}
+- $ setenv PERL5LIB ${BASEDIR}/ensembl/modules:${PERL5LIB}
+- $ setenv PERL5LIB ${BASEDIR}/ensembl-variation/modules:${PERL5LIB}
+- $ setenv PERL5LIB ${BASEDIR}/ensembl-variation/scripts/import:${PERL5LIB}
+- $ setenv PERL5LIB ${BASEDIR}/ensembl-analysis/modules:${PERL5LIB}
++ $ export PERL5LIB=${BASEDIR}/bioperl-live:${PERL5LIB}
++ $ export PERL5LIB=${BASEDIR}/ensembl/modules:${PERL5LIB}
++ $ export PERL5LIB=${BASEDIR}/ensembl-variation/modules:${PERL5LIB}
++ $ export PERL5LIB=${BASEDIR}/ensembl-variation/scripts/import:${PERL5LIB}
++ $ export PERL5LIB=${BASEDIR}/ensembl-analysis/modules:${PERL5LIB}
+
+
+ Configure databases
+--- ensembl-65.orig/htdocs/info/docs/webcode/install/blast.html
++++ ensembl-65/htdocs/info/docs/webcode/install/blast.html
+@@ -35,8 +35,7 @@
+ The Ensembl distribution is usually stored within a filesystem
+ directory (hereafter refered to as $ENSEMBL ROOT), e.g.:
+ </p>
+-<blockquote><pre>$ setenv ENSEMBL_ROOT
+-/usr/local/ensembl</pre></blockquote>
++<blockquote><pre>$ export ENSEMBL_ROOT=/usr/local/ensembl</pre></blockquote>
+
+
+ <p>
+--- ensembl-65.orig/utils/integration/deploy.sh
++++ ensembl-65/utils/integration/deploy.sh
+@@ -1,6 +1,6 @@
+-#! /usr/bin/tcsh
++#!/usr/bin/sh
+
+-setenv CVS_RSH ssh
+-source /localsw/ensembl_web/perlset
++export CVS_RSH=ssh
++. /localsw/ensembl_web/perlset
+
+ /ensemblweb/head/utils/integration/deploy.pl /ensemblweb/head/utils/integration/deploy.yml
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