[med-svn] r17803 - in trunk/packages/mapsembler2/trunk/debian: . patches
Olivier Sallou
osallou at moszumanska.debian.org
Wed Aug 20 06:50:03 UTC 2014
Author: osallou
Date: 2014-08-20 06:50:02 +0000 (Wed, 20 Aug 2014)
New Revision: 17803
Added:
trunk/packages/mapsembler2/trunk/debian/mapsembler2.clean
trunk/packages/mapsembler2/trunk/debian/patches/run_pipeline
Modified:
trunk/packages/mapsembler2/trunk/debian/README.Debian
trunk/packages/mapsembler2/trunk/debian/changelog
trunk/packages/mapsembler2/trunk/debian/mapsembler2.install
trunk/packages/mapsembler2/trunk/debian/mapsembler2.manpages
trunk/packages/mapsembler2/trunk/debian/patches/series
trunk/packages/mapsembler2/trunk/debian/rules
Log:
fix a file conflict with discoSnp, rename binaries
Modified: trunk/packages/mapsembler2/trunk/debian/README.Debian
===================================================================
--- trunk/packages/mapsembler2/trunk/debian/README.Debian 2014-08-19 15:30:44 UTC (rev 17802)
+++ trunk/packages/mapsembler2/trunk/debian/README.Debian 2014-08-20 06:50:02 UTC (rev 17803)
@@ -4,4 +4,4 @@
this package does not contain the visualization component of mapsembler2 due to copyrights of embedded libraries not clearly stated in upstream source.
For usage:
- run_mapsembler_and_phaser -h
+ run_mapsembler2_pipeline -h
Modified: trunk/packages/mapsembler2/trunk/debian/changelog
===================================================================
--- trunk/packages/mapsembler2/trunk/debian/changelog 2014-08-19 15:30:44 UTC (rev 17802)
+++ trunk/packages/mapsembler2/trunk/debian/changelog 2014-08-20 06:50:02 UTC (rev 17803)
@@ -1,3 +1,9 @@
+mapsembler2 (2.2.1+dfsg-2) unstable; urgency=medium
+
+ * Fix kissreads file conflict with discoSnp (Closes: #758648).
+
+ -- Olivier Sallou <osallou at debian.org> Tue, 19 Aug 2014 08:53:07 +0200
+
mapsembler2 (2.2.1+dfsg-1) unstable; urgency=medium
* New upstream release
Added: trunk/packages/mapsembler2/trunk/debian/mapsembler2.clean
===================================================================
--- trunk/packages/mapsembler2/trunk/debian/mapsembler2.clean (rev 0)
+++ trunk/packages/mapsembler2/trunk/debian/mapsembler2.clean 2014-08-20 06:50:02 UTC (rev 17803)
@@ -0,0 +1 @@
+run_mapsembler2_pipeline
Modified: trunk/packages/mapsembler2/trunk/debian/mapsembler2.install
===================================================================
--- trunk/packages/mapsembler2/trunk/debian/mapsembler2.install 2014-08-19 15:30:44 UTC (rev 17802)
+++ trunk/packages/mapsembler2/trunk/debian/mapsembler2.install 2014-08-20 06:50:02 UTC (rev 17803)
@@ -1,6 +1,6 @@
-#maps/mapsembler usr/bin/
+run_mapsembler2_pipeline usr/bin
mapsembler2_extremities/build/mapsembler2_extremities usr/bin/
mapsembler2_extend/mapsembler_extend usr/bin/
#sample_example usr/share/doc/mapsembler2/
-kissreads_graph/kissreads_graph usr/bin/
-kissreads/kissreads usr/bin/
+kissreads_graph/mapsembler2_kissreads_graph usr/bin/
+kissreads/mapsembler2_kissreads usr/bin/
Modified: trunk/packages/mapsembler2/trunk/debian/mapsembler2.manpages
===================================================================
--- trunk/packages/mapsembler2/trunk/debian/mapsembler2.manpages 2014-08-19 15:30:44 UTC (rev 17802)
+++ trunk/packages/mapsembler2/trunk/debian/mapsembler2.manpages 2014-08-20 06:50:02 UTC (rev 17803)
@@ -1,5 +1,6 @@
mapsembler2_extremities.1
mapsembler_extend.1
-kissreads.1
-kissreads_graph.1
+mapsembler2_kissreads.1
+mapsembler2_kissreads_graph.1
+run_mapsembler2_pipeline.1
Added: trunk/packages/mapsembler2/trunk/debian/patches/run_pipeline
===================================================================
--- trunk/packages/mapsembler2/trunk/debian/patches/run_pipeline (rev 0)
+++ trunk/packages/mapsembler2/trunk/debian/patches/run_pipeline 2014-08-20 06:50:02 UTC (rev 17803)
@@ -0,0 +1,60 @@
+Author: Olivier Sallou <osallou at debian.org>
+Subject: use default PATH
+Description: use tools in path instead of local dirs as upstream
+Last-Updated: 2014-08-20
+Forwarded: no
+Index: mapsembler2_pipeline/run_mapsembler2_pipeline.sh
+===================================================================
+--- mapsembler2_pipeline.orig/run_mapsembler2_pipeline.sh
++++ mapsembler2_pipeline/run_mapsembler2_pipeline.sh
+@@ -16,7 +16,7 @@ t=0
+ f=1 #kind of process (search mode 1=Breadth and 2=Depth)
+ x=40 #node length limit
+ y=10000 #graph depth limit
+-PATH_TOOLS="./tools/" # path were executables mapsembler and phaser are. Leave blank if they are located in a directory located in the PATH environnement variable
++PATH_TOOLS="" # path were executables mapsembler and phaser are. Leave blank if they are located in a directory located in the PATH environnement variable
+ #######################################################################
+ #################### END HEADER #######################
+ #######################################################################
+@@ -211,20 +211,20 @@ fi
+ if [ $t -gt 2 ]
+ then
+ echo -e "\n"
+- echo -e "\033[31m running $PATH_TOOLS""kissreads_graph $prefix_results\_k_$k\_c_$c\_t_$t.json $read_sets -k $k -c $c -t m -M -o $prefix_results\_k_$k\_c_$c\_t_$t\_modified.json\033[0m"
+-$PATH_TOOLS\kissreads_graph $prefix_results\_k_$k\_c_$c\_t_$t.json $read_sets -k $k -c $c -t m -M -o $prefix_results\_k_$k\_c_$c\_t_$t\_modified.json
++ echo -e "\033[31m running $PATH_TOOLS""mapsembler2_kissreads_graph $prefix_results\_k_$k\_c_$c\_t_$t.json $read_sets -k $k -c $c -t m -M -o $prefix_results\_k_$k\_c_$c\_t_$t\_modified.json\033[0m"
++$PATH_TOOLS\mapsembler2_kissreads_graph $prefix_results\_k_$k\_c_$c\_t_$t.json $read_sets -k $k -c $c -t m -M -o $prefix_results\_k_$k\_c_$c\_t_$t\_modified.json
+ if [ $? -ne 0 ]
+ then
+- echo "there was a problem with kissreads_graph"
++ echo "there was a problem with mapsembler2_kissreads_graph"
+ exit
+ fi
+
+ echo -e "\n"
+- echo -e "\033[31m $PATH_TOOLS""kissreads_graph $prefix_results\_k_$k\_c_$c\_t_$t\_modified.json $read_sets -k $k -c $c -t c -M -o $prefix_results\_k_$k\_c_$c\_t_$t\_modified_and_covered.json\033[0m"
+-$PATH_TOOLS\kissreads_graph $prefix_results\_k_$k\_c_$c\_t_$t\_modified.json $read_sets -k $k -c $c -t c -M -o $prefix_results\_k_$k\_c_$c\_t_$t\_modified_and_covered.json
++ echo -e "\033[31m $PATH_TOOLS""mapsembler2_kissreads_graph $prefix_results\_k_$k\_c_$c\_t_$t\_modified.json $read_sets -k $k -c $c -t c -M -o $prefix_results\_k_$k\_c_$c\_t_$t\_modified_and_covered.json\033[0m"
++$PATH_TOOLS\mapsembler2_kissreads_graph $prefix_results\_k_$k\_c_$c\_t_$t\_modified.json $read_sets -k $k -c $c -t c -M -o $prefix_results\_k_$k\_c_$c\_t_$t\_modified_and_covered.json
+ if [ $? -ne 0 ]
+ then
+- echo "there was a problem with kissreads_graph"
++ echo "there was a problem with mapsembler2_kissreads_graph"
+ exit
+ fi
+
+@@ -232,11 +232,11 @@ $PATH_TOOLS\kissreads_graph $prefix_resu
+
+ else
+ echo -e "\n"
+- echo -e "\033[31m running $PATH_TOOLS""kissreads $prefix_results\_k_$k\_c_$c\_t_$t.fasta $read_sets -f -o $prefix_results\_coherent_k_$k\_c_$c\_t_$t.fasta -u $prefix_results\_uncoherent_k_$k\_c_$c\_t_$t.fasta\033[0m"
+-$PATH_TOOLS\kissreads $prefix_results\_k_$k\_c_$c\_t_$t.fasta $read_sets -k $k -c $c -d $d -f -o $prefix_results\_coherent_k_$k\_c_$c\_t_$t.fasta -u $prefix_results\_uncoherent_k_$k\_c_$c\_t_$t.fasta
++ echo -e "\033[31m running $PATH_TOOLS""mapsembler2_kissreads $prefix_results\_k_$k\_c_$c\_t_$t.fasta $read_sets -f -o $prefix_results\_coherent_k_$k\_c_$c\_t_$t.fasta -u $prefix_results\_uncoherent_k_$k\_c_$c\_t_$t.fasta\033[0m"
++$PATH_TOOLS\mapsembler2_kissreads $prefix_results\_k_$k\_c_$c\_t_$t.fasta $read_sets -k $k -c $c -d $d -f -o $prefix_results\_coherent_k_$k\_c_$c\_t_$t.fasta -u $prefix_results\_uncoherent_k_$k\_c_$c\_t_$t.fasta
+ if [ $? -ne 0 ]
+ then
+- echo "there was a problem with kissreads"
++ echo "there was a problem with mapsembler2_kissreads"
+ exit
+ fi
+
Modified: trunk/packages/mapsembler2/trunk/debian/patches/series
===================================================================
--- trunk/packages/mapsembler2/trunk/debian/patches/series 2014-08-19 15:30:44 UTC (rev 17802)
+++ trunk/packages/mapsembler2/trunk/debian/patches/series 2014-08-20 06:50:02 UTC (rev 17803)
@@ -1,2 +1,3 @@
use_debian_libs
add_hardening
+run_pipeline
Modified: trunk/packages/mapsembler2/trunk/debian/rules
===================================================================
--- trunk/packages/mapsembler2/trunk/debian/rules 2014-08-19 15:30:44 UTC (rev 17802)
+++ trunk/packages/mapsembler2/trunk/debian/rules 2014-08-20 06:50:02 UTC (rev 17803)
@@ -39,7 +39,11 @@
override_dh_install:
help2man --help-option=-h --no-discard-stderr --version-string=$(SRC_VERSION) ./mapsembler2_extremities/build/mapsembler2_extremities > mapsembler2_extremities.1
help2man --help-option=-h --no-discard-stderr --version-string=$(SRC_VERSION) ./mapsembler2_extend/mapsembler_extend > mapsembler_extend.1
- help2man --help-option=-h --no-discard-stderr --version-string=$(SRC_VERSION) ./kissreads/kissreads > kissreads.1
- help2man --help-option=-h --no-discard-stderr --version-string=$(SRC_VERSION) ./kissreads_graph/kissreads_graph > kissreads_graph.1
+ mv ./kissreads/kissreads ./kissreads/mapsembler2_kissreads
+ help2man --help-option=-h --no-discard-stderr --version-string=$(SRC_VERSION) ./kissreads/mapsembler2_kissreads > mapsembler2_kissreads.1
+ mv ./kissreads_graph/kissreads_graph ./kissreads_graph/mapsembler2_kissreads_graph
+ help2man --help-option=-h --no-discard-stderr --version-string=$(SRC_VERSION) ./kissreads_graph/mapsembler2_kissreads_graph > mapsembler2_kissreads_graph.1
+ cp run_mapsembler2_pipeline.sh run_mapsembler2_pipeline
+ help2man --help-option=-h --no-discard-stderr --version-string=$(SRC_VERSION) run_mapsembler2_pipeline > run_mapsembler2_pipeline.1
dh_install
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