Gapfiller 1.10 f01 (#9163)
* GapFiller.pl fixes: line endings, env perl, convert to Getopt::Std, requires perl with threads. * GapFiller.pl fixed source path, install location. * Fixed missing space.
This commit is contained in:
parent
d6daa8fab5
commit
e9863f56f3
@ -24,6 +24,7 @@
|
|||||||
##############################################################################
|
##############################################################################
|
||||||
from spack import *
|
from spack import *
|
||||||
import os
|
import os
|
||||||
|
import glob
|
||||||
|
|
||||||
|
|
||||||
class Gapfiller(Package):
|
class Gapfiller(Package):
|
||||||
@ -44,9 +45,20 @@ def url_for_version(self, version):
|
|||||||
return "file://{0}/39GapFiller_v{1}_linux-x86_64.tar.gz".format(
|
return "file://{0}/39GapFiller_v{1}_linux-x86_64.tar.gz".format(
|
||||||
os.getcwd(), version.dashed)
|
os.getcwd(), version.dashed)
|
||||||
|
|
||||||
depends_on('perl', type=('build', 'run'))
|
depends_on('perl+threads', type=('build', 'run'))
|
||||||
|
|
||||||
|
def patch(self):
|
||||||
|
with working_dir('.'):
|
||||||
|
files = glob.iglob("*.pl")
|
||||||
|
for file in files:
|
||||||
|
change = FileFilter(file)
|
||||||
|
change.filter('usr/bin/perl', 'usr/bin/env perl')
|
||||||
|
change.filter('require "getopts.pl";', 'use Getopt::Std;')
|
||||||
|
change.filter('&Getopts', 'getopts')
|
||||||
|
change.filter('\r', '')
|
||||||
|
set_executable(file)
|
||||||
|
|
||||||
def install(self, spec, prefix):
|
def install(self, spec, prefix):
|
||||||
install_tree('bowtie', prefix.bowtie)
|
install_tree('bowtie', prefix.bin.bowtie)
|
||||||
install_tree('bwa', prefix.bwa)
|
install_tree('bwa', prefix.bin.bwa)
|
||||||
install('GapFiller.pl', prefix)
|
install('GapFiller.pl', prefix.bin)
|
||||||
|
Loading…
Reference in New Issue
Block a user