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| author |   Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2013-09-11 22:17:32 +0200 |
|---|---|---|
| committer | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2013-09-11 22:17:32 +0200 |
| commit | b3968be9936f8466a7dacb0ded98ac1c79622738 (patch) | |
| tree | 00a8dcfbe067facf3a572637e9cf98cde7b4bc8e /sci-biology/amos/files | |
| parent | final clean up (diff) | |
| download | sci-b3968be9936f8466a7dacb0ded98ac1c79622738.tar.gz sci-b3968be9936f8466a7dacb0ded98ac1c79622738.tar.bz2 sci-b3968be9936f8466a7dacb0ded98ac1c79622738.zip | |
Fix indentation error and remove unused import of string module (there could be more cleanup as suggested by pychecker). Credits to http://sourceforge.net/p/amos/support-requests/1/
Package-Manager: portage-2.1.12.2
Diffstat (limited to 'sci-biology/amos/files')
| -rw-r--r-- | sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch | 15 | ||||
| -rw-r--r-- | sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch | 25 |
2 files changed, 40 insertions, 0 deletions
diff --git a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch new file mode 100644 index 000000000..de2a41184 --- /dev/null +++ b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch @@ -0,0 +1,15 @@ + src/Align/find-tandem.cc | 1 + + 1 files changed, 1 insertions(+), 0 deletions(-) + +diff --git a/src/Align/find-tandem.cc b/src/Align/find-tandem.cc +index ddf1cab..a29e21e 100644 +--- a/src/Align/find-tandem.cc ++++ b/src/Align/find-tandem.cc +@@ -7,6 +7,7 @@ + #include <vector> + #include <ctime> + #include <sys/time.h> ++#include <unistd.h> + using namespace std; + + const int OFFSET_TABLE_SIZE = 100; diff --git a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch new file mode 100644 index 000000000..97a8f59d0 --- /dev/null +++ b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch @@ -0,0 +1,25 @@ +--- amos-3.1.0/src/Pipeline/goBambus2.py.orig 2013-09-11 01:05:29.850090457 +0200 ++++ amos-3.1.0/src/Pipeline/goBambus2.py 2013-09-11 01:07:03.250090701 +0200 +@@ -1,7 +1,7 @@ + #pipeline script for assembly + Bambus 2 + #contributed by Todd J Treangen + +-import string, sys, os, subprocess#, spincursor ++import sys, os, subprocess#, spincursor + + RED = "\033[0;31m" + GREEN = "\033[0;32m" +@@ -360,7 +360,7 @@ + print "\t\t%s...failed%s"%(RED,NONE) + sys.exit(1) + +- p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) ++ p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) + + if xopt_dict["verbose"] == 1: + print "10) running OutputResults" +@@ -388,4 +388,3 @@ + else: + print "\t\t%s...failed%s"%(RED,NONE) + sys.exit(1) +-) |