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Gapfiller 1.10 f01 (#9163)

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* 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:
Aronnax, Miles V. [ISU/LAS] 2018-09-28 14:45:54 -05:00 committed by Levi Baber
parent d6daa8fab5
commit e9863f56f3
1 changed files with 16 additions and 4 deletions
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20
var/spack/repos/builtin/packages/gapfiller/package.py
View File

@ -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)