[med-svn] r9102 - in trunk/packages/ensembl/ensembl/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Sun Dec 25 23:03:07 UTC 2011
Author: tille
Date: 2011-12-25 23:03:07 +0000 (Sun, 25 Dec 2011)
New Revision: 9102
Added:
trunk/packages/ensembl/ensembl/trunk/debian/patches/do_not_advertise_csh.patch
Modified:
trunk/packages/ensembl/ensembl/trunk/debian/changelog
trunk/packages/ensembl/ensembl/trunk/debian/patches/series
Log:
Adde lintian override for /tmp usage; do not advertise usage of csh in documentation
Modified: trunk/packages/ensembl/ensembl/trunk/debian/changelog
===================================================================
--- trunk/packages/ensembl/ensembl/trunk/debian/changelog 2011-12-25 18:25:45 UTC (rev 9101)
+++ trunk/packages/ensembl/ensembl/trunk/debian/changelog 2011-12-25 23:03:07 UTC (rev 9102)
@@ -54,6 +54,14 @@
* debian/ensembl.{config,postinst}: Properly initialise debconf
* debian/ensembl.preinst: Removed because empty (except dh-make
templates)
+ * debian/ensembl.lintian-overrides: Override warning
+ possibly-insecure-handling-of-tmp-files-in-maintainer-script
+ However, this should be discussed with upstream
+ * debian/patches/do_not_advertise_csh.patch: Several documentation
+ files are advertising csh to some extend (one is also warning that
+ csh is not tested). Because csh-considered-harmful we do not like
+ to advertise csh for no need at all and the patch is just dropping
+ csh references.
-- Andreas Tille <tille at debian.org> Thu, 15 Dec 2011 19:01:29 +0100
Added: trunk/packages/ensembl/ensembl/trunk/debian/patches/do_not_advertise_csh.patch
===================================================================
--- trunk/packages/ensembl/ensembl/trunk/debian/patches/do_not_advertise_csh.patch (rev 0)
+++ trunk/packages/ensembl/ensembl/trunk/debian/patches/do_not_advertise_csh.patch 2011-12-25 23:03:07 UTC (rev 9102)
@@ -0,0 +1,195 @@
+Author: Andreas Tille <tille at debian.org>
+Date: Thu, 15 Dec 2011 19:01:29 +0100
+Description: Do not advertise csh usage
+ Several documentation files are advertising csh to some extend (one is
+ also warning that csh is not tested). Because csh-considered-harmful we
+ do not like to advertise csh for no need at all and the patch is just
+ dropping csh references.
+
+--- ensembl-65.orig/ensembl/docs/tutorial/ensembl_tutorial.txt
++++ ensembl-65/ensembl/docs/tutorial/ensembl_tutorial.txt
+@@ -83,12 +83,7 @@
+
+ Setting up the Environment
+
+-Perl needs to know the location of the BioPerl and Ensembl API modules in order for any scripts that you write to work. You can do this by setting the PERL5LIB environment variable from your shell. Assuming that you have placed the source in an src directory under your home directory the following tcsh/csh commands could be used:
+-
+-setenv PERL5LIB ${PERL5LIB}:${HOME}/src/bioperl-live
+-setenv PERL5LIB ${PERL5LIB}:${HOME}/src/ensembl/modules
+-
+-The same example in bash would be:
++Perl needs to know the location of the BioPerl and Ensembl API modules in order for any scripts that you write to work. You can do this by setting the PERL5LIB environment variable from your shell. Assuming that you have placed the source in an src directory under your home directory the following shell commands could be used:
+
+ export PERL5LIB=${PERL5LIB}:${HOME}/src/bioperl-live
+ export PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl/modules
+--- ensembl-65.orig/ensembl/modules/t/README
++++ ensembl-65/ensembl/modules/t/README
+@@ -6,10 +6,6 @@
+ module ensembl-test. To use the tests you must add the ensembl-test
+ modules to your PERL5LIB environment variable.
+
+- Example (for tcsh or csh):
+-
+- setenv PERL5LIB ${PERL5LIB}:${ENSHOME}/ensembl-test/modules
+-
+ Example (for ksh or bash):
+
+ export PERL5LIB=${PERL5LIB}:${ENSHOME}/ensembl-test/modules
+--- ensembl-65.orig/ensembl-compara/docs/ComparaTutorial.txt
++++ ensembl-65/ensembl-compara/docs/ComparaTutorial.txt
+@@ -21,12 +21,8 @@
+
+ This will check out ensembl-compara code for stable branch 51. Make sure the EnsEMBL core code you have already checked out is on the same branch. Note that the branch that is checked out should correspond to the database version being used. Thus ensembl_compara_51 and e.g. homo_sapiens_core_51_36m and mus_musculus_core_51_37d should be used with the above ensembl branch 51 code.
+ Environment Variables
+-The following PERL5LIB environment variables should be set up:
+-- under tcsh/csh shell with
+-setenv PERL5LIB ${PERL5LIB}:{HOME}/src/bioperl-live: \
+-${HOME}/src/ensembl/modules:${HOME}/src/ensembl-compara/modules
++The following PERL5LIB environment variables should be set up under bash shell with:
+
+-- under bash shell with
+ export PERL5LIB=${PERL5LIB}:{HOME}/src/bioperl-live: \
+ ${HOME}/src/ensembl/modules:${HOME}/src/ensembl-compara/modules
+
+--- ensembl-65.orig/ensembl-compara/scripts/view_alignment/view_alignment.pl
++++ ensembl-65/ensembl-compara/scripts/view_alignment/view_alignment.pl
+@@ -33,10 +33,6 @@
+
+ export PATH=/nfs/sids/badger/OSF/STADEN_PKGS/unix-rel-1-7-0/linux-x86_64-bin:$HOME/src/ensembl_main/ensembl_compara/scripts/view_alignment:$PATH
+
+-in csh:
+-
+-setenv PATH /nfs/sids/badger/OSF/STADEN_PKGS/unix-rel-1-7-0/linux-x86_64-bin:$HOME/src/ensembl_main/ensembl_compara/scripts/view_alignment:$PATH
+-
+ It must also be run under X windows.
+
+ =head1 SYNPOSIS
+--- ensembl-65.orig/ensembl-compara/scripts/pipeline/README-genetree
++++ ensembl-65/ensembl-compara/scripts/pipeline/README-genetree
+@@ -124,17 +124,6 @@
+ Beware the pipeline has been seen to misbehave when using csh, and
+ is mostly tested under bash terminals.
+
+-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}
+ $ export PERL5LIB=${BASEDIR}/ensembl-compara/modules:${PERL5LIB}
+@@ -336,10 +325,9 @@
+ 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:${BLASTFILTER}
+
+
+ 5- Create the species tree file
+@@ -587,13 +575,11 @@
+ in one's path. This can be done by either extending PATH or linking the
+ scripts to an existing directory in the PATH
+
+- tcsh$ 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/htdocs/info/docs/api/api_installation.html
++++ ensembl-65/htdocs/info/docs/api/api_installation.html
+@@ -116,20 +116,6 @@
+
+ <li>
+ <p>
+-Under <kbd>csh</kbd> or <kbd>tcsh</kbd>:
+-</p>
+-
+-<pre>
+-setenv PERL5LIB ${PERL5LIB}:${HOME}/src/bioperl-live
+-setenv PERL5LIB ${PERL5LIB}:${HOME}/src/ensembl/modules
+-setenv PERL5LIB ${PERL5LIB}:${HOME}/src/ensembl-compara/modules
+-setenv PERL5LIB ${PERL5LIB}:${HOME}/src/ensembl-variation/modules
+-setenv PERL5LIB ${PERL5LIB}:${HOME}/src/ensembl-functgenomics/modules
+-</pre>
+-</li>
+-
+-<li>
+-<p>
+ Under Windows (assuming you installed the APIs in C:\src\):
+ </p>
+
+--- ensembl-65.orig/htdocs/info/docs/api/registry.html
++++ ensembl-65/htdocs/info/docs/api/registry.html
+@@ -175,14 +175,6 @@
+ </pre>
+ </li>
+
+-<li>
+-Under csh or tcsh:
+-
+-<pre class="code">
+-setenv ENSEMBL_REGISTRY "/usr/local/share/ensembl_registry.conf"
+-</pre>
+-</li>
+-
+ </ul>
+
+
+--- ensembl-65.orig/htdocs/info/docs/webcode/install/non-ensembl-code.html
++++ ensembl-65/htdocs/info/docs/webcode/install/non-ensembl-code.html
+@@ -309,8 +309,8 @@
+ SGI_4 SGI_4_GCC SGI_4_IRIX5 SGI_4_PURE SGI_5_GCC SGI_65_GCC_DEF
+ SOLARIS_4 SOLARIS_4_OPT SOLARIS_4_RELEASE SUN_4_DEF
+ WIN32_4</kbd>
+-<p>For example (in csh):</p>
+-<pre class="code">setenv ACEDB_MACHINE SOLARIS_4</pre>
++<p>For example:</p>
++<pre class="code">export ACEDB_MACHINE=SOLARIS_4</pre>
+ <p>Consult the AceDB documentation if you need more help.</p>
+
+ <p>If you wish to use the GTK/readline packages distributed with acedb you should build them before
+--- ensembl-65.orig/public-plugins/ensembl/htdocs/info/docs/eHive/installation.html
++++ ensembl-65/public-plugins/ensembl/htdocs/info/docs/eHive/installation.html
+@@ -45,10 +45,6 @@
+ using bash syntax (for best results, append this line to your ~/.bashrc configuration file):
+ <PRE>$ export ENSEMBL_CVS_ROOT_DIR="$HOME/ensembl_main"</PRE>
+ </LI>
+-<LI>
+-using [t]csh syntax (for best results, append this line to your ~/.cshrc or ~/.tcshrc configuration file):
+-<PRE>$ setenv ENSEMBL_CVS_ROOT_DIR "$HOME/ensembl_main"</PRE>
+-</LI>
+ </UL>
+ </LI>
+
+@@ -89,14 +85,6 @@
+ $ export PERL5LIB=${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/ensembl-compara/modules # optional but recommended, see previous point.
+ </PRE>
+ </LI>
+-<LI>
+-using [t]csh syntax (for best results, append these lines to your ~/.cshrc or ~/.tcshrc configuration file):
+-<PRE>$ setenv PERL5LIB ${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/bioperl-live
+-$ setenv PERL5LIB ${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/ensembl/modules
+-$ setenv PERL5LIB ${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/ensembl-hive/modules
+-$ setenv PERL5LIB ${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/ensembl-compara/modules # optional but recommended, see previous point.
+-</PRE>
+-</LI>
+ </UL>
+ </LI>
+ </OL>
Modified: trunk/packages/ensembl/ensembl/trunk/debian/patches/series
===================================================================
--- trunk/packages/ensembl/ensembl/trunk/debian/patches/series 2011-12-25 18:25:45 UTC (rev 9101)
+++ trunk/packages/ensembl/ensembl/trunk/debian/patches/series 2011-12-25 23:03:07 UTC (rev 9102)
@@ -7,3 +7,4 @@
httpd.patch
SiteDefs_tmpdir.patch
fix_usr_bin_env_typo.patch
+do_not_advertise_csh.patch
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