[med-svn] r16753 - in trunk/packages/staden/trunk/debian: . bin patches
Andreas Tille
tille at moszumanska.debian.org
Tue Apr 22 15:07:24 UTC 2014
Author: tille
Date: 2014-04-22 15:07:24 +0000 (Tue, 22 Apr 2014)
New Revision: 16753
Added:
trunk/packages/staden/trunk/debian/clean
Removed:
trunk/packages/staden/trunk/debian/patches/1001_fix_zlib_linkage.patch
Modified:
trunk/packages/staden/trunk/debian/bin/staden
trunk/packages/staden/trunk/debian/changelog
trunk/packages/staden/trunk/debian/patches/enable_setting_stadenroot.patch
trunk/packages/staden/trunk/debian/patches/series
trunk/packages/staden/trunk/debian/rules
Log:
Make sure you can build twice in a row; several fixes regarding the wrapper structure; remove now useless patch; do not remove binary file which is actually needed; update TODO list in d/changelog
Modified: trunk/packages/staden/trunk/debian/bin/staden
===================================================================
--- trunk/packages/staden/trunk/debian/bin/staden 2014-04-22 14:49:20 UTC (rev 16752)
+++ trunk/packages/staden/trunk/debian/bin/staden 2014-04-22 15:07:24 UTC (rev 16753)
@@ -1,7 +1,13 @@
#!/bin/sh
BINDIR=/usr/lib/staden/bin
+
+# make sure tools like tg_index.bin will be found
+export PATH=$BINDIR:$PATH
export STADENROOT=/usr
+## stash fails to load if these variables are not set
+export STADLIB=$STADENROOT/lib/staden/
+export STADTABL=$STADENROOT/share/staden/etc
if [ $# -lt 1 ] ; then
echo "Usage: $0 <program>" 1>&2
Modified: trunk/packages/staden/trunk/debian/changelog
===================================================================
--- trunk/packages/staden/trunk/debian/changelog 2014-04-22 14:49:20 UTC (rev 16752)
+++ trunk/packages/staden/trunk/debian/changelog 2014-04-22 15:07:24 UTC (rev 16753)
@@ -1,9 +1,24 @@
staden (2.0.0+b10-1) UNRELEASED; urgency=low
FIXME: TODO
- Help does not work because of missing files
- couldn't open "/usr/share/doc/staden/manual/gap4.index": no such file or directory
+ * Help does not work because of missing files
+ couldn't open "/usr/share/doc/staden/manual/gap4.index": no such file or directory
+ * $ staden spin
+ <date> EMBOSS: data directory not found
+ * $ staden create_emboss_files
+ no files matched glob pattern "/*.acd"
+ while executing
+ "glob $acd_dir/*.acd"
+ (procedure "process_files" line 3)
+ invoked from within
+ "process_files $acd_dir $acdtcl_dir"
+ (file "/usr/share/staden/tcl/spin_emboss/create_emboss_files.tcl" line 140)
+ Hint: spin_emboss/create_emboss_files.tcl:
+ set acd [file dirname $dir]/../share/EMBOSS/acd
+ I somehow suspect that /share/EMBOSS needs to be dropped
+
+
[ Tim Booth ]
* Initial release to Debian (Closes: #710324)
Added: trunk/packages/staden/trunk/debian/clean
===================================================================
--- trunk/packages/staden/trunk/debian/clean (rev 0)
+++ trunk/packages/staden/trunk/debian/clean 2014-04-22 15:07:24 UTC (rev 16753)
@@ -0,0 +1,10 @@
+copy_reads/copy_reads
+gap4/gap4
+gap5/gap5
+gap5/gap5_cmd
+gap5/tg_index
+gap5/tg_view
+prefinish/prefinish
+pregap4/pregap4
+spin/spin
+trev/trev
Deleted: trunk/packages/staden/trunk/debian/patches/1001_fix_zlib_linkage.patch
===================================================================
--- trunk/packages/staden/trunk/debian/patches/1001_fix_zlib_linkage.patch 2014-04-22 14:49:20 UTC (rev 16752)
+++ trunk/packages/staden/trunk/debian/patches/1001_fix_zlib_linkage.patch 2014-04-22 15:07:24 UTC (rev 16753)
@@ -1,15 +0,0 @@
-Author: Jonas Smedegaard <dr at jones.dk>
-Last-Update: Wed, 29 May 2013 15:22:02 +0200
-Description: Fix usage of zlib
-
---- a/gap5/zfio.h
-+++ b/gap5/zfio.h
-@@ -9,7 +9,7 @@
- */
- typedef struct {
- FILE *fp;
-- gzFile *gz;
-+ gzFile gz;
- } zfp;
-
- off_t zftello(zfp *zf);
Modified: trunk/packages/staden/trunk/debian/patches/enable_setting_stadenroot.patch
===================================================================
--- trunk/packages/staden/trunk/debian/patches/enable_setting_stadenroot.patch 2014-04-22 14:49:20 UTC (rev 16752)
+++ trunk/packages/staden/trunk/debian/patches/enable_setting_stadenroot.patch 2014-04-22 15:07:24 UTC (rev 16753)
@@ -4,37 +4,37 @@
file when installed to the location where the wrapper will seek for
the scripts
---- staden-2.0.0b10-src.orig/gap5/gap5.in
-+++ staden-2.0.0b10-src/gap5/gap5.in
-@@ -67,7 +67,10 @@
+--- a/gap5/gap5.in
++++ b/gap5/gap5.in
+@@ -67,7 +67,10 @@ find_dir() {
echo $dir
}
-STADENROOT=`find_dir $0`/..; export STADENROOT
+STADENROOT=${STADENROOT:-`find_dir $0`/..}; export STADENROOT
+if [ ! -f "$STADENROOT"/share/staden/staden.profile ] ; then
-+ STADENROOT=/usr
++ STADENROOT=/usr
+fi
STADEN_PREPEND=1; export STADEN_PREPEND
. "$STADENROOT"/share/staden/staden.profile
---- staden-2.0.0b10-src.orig/gap4/gap4.in
-+++ staden-2.0.0b10-src/gap4/gap4.in
-@@ -67,7 +67,10 @@
+--- a/gap4/gap4.in
++++ b/gap4/gap4.in
+@@ -67,7 +67,10 @@ find_dir() {
echo $dir
}
-STADENROOT=`find_dir $0`/..; export STADENROOT
+STADENROOT=${STADENROOT:-`find_dir $0`/..}; export STADENROOT
+if [ ! -f "$STADENROOT"/share/staden/staden.profile ] ; then
-+ STADENROOT=/usr
++ STADENROOT=/usr
+fi
STADEN_PREPEND=1; export STADEN_PREPEND
. "$STADENROOT"/share/staden/staden.profile
---- staden-2.0.0b10-src.orig/pregap4/pregap4.in
-+++ staden-2.0.0b10-src/pregap4/pregap4.in
-@@ -67,7 +67,10 @@
+--- a/pregap4/pregap4.in
++++ b/pregap4/pregap4.in
+@@ -67,7 +67,10 @@ find_dir() {
echo $dir
}
@@ -46,9 +46,9 @@
STADEN_PREPEND=1; export STADEN_PREPEND
. "$STADENROOT"/share/staden/staden.profile
---- staden-2.0.0b10-src.orig/spin/spin.in
-+++ staden-2.0.0b10-src/spin/spin.in
-@@ -67,7 +67,10 @@
+--- a/spin/spin.in
++++ b/spin/spin.in
+@@ -67,7 +67,10 @@ find_dir() {
echo $dir
}
@@ -60,9 +60,9 @@
STADEN_PREPEND=1; export STADEN_PREPEND
. "$STADENROOT"/share/staden/staden.profile
---- staden-2.0.0b10-src.orig/trev/trev.in
-+++ staden-2.0.0b10-src/trev/trev.in
-@@ -70,7 +70,10 @@
+--- a/trev/trev.in
++++ b/trev/trev.in
+@@ -70,7 +70,10 @@ find_dir() {
#
# Run it!
#
@@ -74,3 +74,101 @@
STADEN_PREPEND=1; export STADEN_PREPEND
. "$STADENROOT"/share/staden/staden.profile
+--- a/gap5/gap5_cmd.in
++++ b/gap5/gap5_cmd.in
+@@ -67,7 +67,10 @@ find_dir() {
+ echo $dir
+ }
+
+-STADENROOT=`find_dir $0`/..; export STADENROOT
++STADENROOT=${STADENROOT:-`find_dir $0`/..}; export STADENROOT
++if [ ! -f "$STADENROOT"/share/staden/staden.profile ] ; then
++ STADENROOT=/usr
++fi
+ STADEN_PREPEND=1; export STADEN_PREPEND
+ . "$STADENROOT"/share/staden/staden.profile
+
+--- a/gap5/tg_index.in
++++ b/gap5/tg_index.in
+@@ -67,7 +67,10 @@ find_dir() {
+ echo $dir
+ }
+
+-STADENROOT=`find_dir $0`/..; export STADENROOT
++STADENROOT=${STADENROOT:-`find_dir $0`/..}; export STADENROOT
++if [ ! -f "$STADENROOT"/share/staden/staden.profile ] ; then
++ STADENROOT=/usr
++fi
+ STADEN_PREPEND=1; export STADEN_PREPEND
+ . "$STADENROOT"/share/staden/staden.profile
+
+--- a/gap5/tg_view.in
++++ b/gap5/tg_view.in
+@@ -67,7 +67,10 @@ find_dir() {
+ echo $dir
+ }
+
+-STADENROOT=`find_dir $0`/..; export STADENROOT
++STADENROOT=${STADENROOT:-`find_dir $0`/..}; export STADENROOT
++if [ ! -f "$STADENROOT"/share/staden/staden.profile ] ; then
++ STADENROOT=/usr
++fi
+ STADEN_PREPEND=1; export STADEN_PREPEND
+ . "$STADENROOT"/share/staden/staden.profile
+
+--- a/prefinish/finish_sanger
++++ b/prefinish/finish_sanger
+@@ -70,7 +70,10 @@ find_dir() {
+ #
+ # Run it!
+ #
+-STADENROOT=`find_dir $0`/..; export STADENROOT
++STADENROOT=${STADENROOT:-`find_dir $0`/..}; export STADENROOT
++if [ ! -f "$STADENROOT"/share/staden/staden.profile ] ; then
++ STADENROOT=/usr
++fi
+ STADLIB=$STADENROOT/lib/staden/; export STADLIB
+ STADTABL=$STADENROOT/share/staden/etc; export STADTABL
+ STADTCL=$STADENROOT/share/staden/tcl; export STADTCL
+--- a/prefinish/prefinish.in
++++ b/prefinish/prefinish.in
+@@ -70,7 +70,10 @@ find_dir() {
+ #
+ # Run it!
+ #
+-STADENROOT=`find_dir $0`/..; export STADENROOT
++STADENROOT=${STADENROOT:-`find_dir $0`/..}; export STADENROOT
++if [ ! -f "$STADENROOT"/share/staden/staden.profile ] ; then
++ STADENROOT=/usr
++fi
+ STADEN_PREPEND=1; export STADEN_PREPEND
+ . "$STADENROOT"/share/staden/staden.profile
+
+--- a/copy_reads/copy_reads.in
++++ b/copy_reads/copy_reads.in
+@@ -67,7 +67,10 @@ find_dir() {
+ echo $dir
+ }
+
+-STADENROOT=`find_dir $0`/..; export STADENROOT
++STADENROOT=${STADENROOT:-`find_dir $0`/..}; export STADENROOT
++if [ ! -f "$STADENROOT"/share/staden/staden.profile ] ; then
++ STADENROOT=/usr
++fi
+ STADEN_PREPEND=1; export STADEN_PREPEND
+ . "$STADENROOT"/share/staden/staden.profile
+
+--- a/spin_emboss/create_emboss_files
++++ b/spin_emboss/create_emboss_files
+@@ -70,7 +70,10 @@ find_dir() {
+ #
+ # Run it!
+ #
+-STADENROOT=`find_dir $0`/..; export STADENROOT
++STADENROOT=${STADENROOT:-`find_dir $0`/..}; export STADENROOT
++if [ ! -f "$STADENROOT"/share/staden/staden.profile ] ; then
++ STADENROOT=/usr
++fi
+ STADLIB=$STADENROOT/lib/staden/; export STADLIB
+ STADTABL=$STADENROOT/share/staden/etc; export STADTABL
+ STADTCL=$STADENROOT/share/staden/tcl; export STADTCL
Modified: trunk/packages/staden/trunk/debian/patches/series
===================================================================
--- trunk/packages/staden/trunk/debian/patches/series 2014-04-22 14:49:20 UTC (rev 16752)
+++ trunk/packages/staden/trunk/debian/patches/series 2014-04-22 15:07:24 UTC (rev 16753)
@@ -1,4 +1,3 @@
-# 1001_fix_zlib_linkage.patch
# remove_svnversion_dep.patch
make_help_menus_work.patch
hardening_format-security.patch
Modified: trunk/packages/staden/trunk/debian/rules
===================================================================
--- trunk/packages/staden/trunk/debian/rules 2014-04-22 14:49:20 UTC (rev 16752)
+++ trunk/packages/staden/trunk/debian/rules 2014-04-22 15:07:24 UTC (rev 16753)
@@ -13,10 +13,6 @@
override_dh_auto_install:
dh_auto_install
- #These are identical to the files without the extension.
- #If I really need them I'll symlink them, or better patch the
- #code to not need them.
- rm -f debian/*/usr/bin/*.bin
# Remove file causing lintian errors that is targeting at windows
find debian -name help_windows.tcl -delete
# Remove some empty directories
@@ -35,6 +31,8 @@
override_dh_fixperms:
dh_fixperms
# scripts should be executable
+ chmod a+x debian/*/usr/share/staden/tcl/gap5/contig_graph.tcl
+ chmod a+x debian/*/usr/share/staden/tcl/gap5/gap5_cmd.tcl
chmod a+x debian/*/usr/share/staden/tcl/prefinish/add_stops.tcl
chmod a+x debian/*/usr/share/staden/tcl/prefinish/finish_sanger.tcl
chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_ext.tcl
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