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bcl2fastq2: package update (#7794)

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* bcl2fastq2: package update

* package/bcl2fastq2: homepage fix

* package/bcl2fastq2: glob fix

* package/bcl2fastq2: code clean up

* package/bcl2fastq2: code clean up #2
This commit is contained in:
Matteo Guglielmi 2018-04-18 17:11:44 +02:00 committed by Adam J. Stewart
parent 87747b888f
commit 247f24e015
1 changed files with 10 additions and 9 deletions
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19
var/spack/repos/builtin/packages/bcl2fastq2/package.py
View file

@ -25,6 +25,7 @@
from spack import *
import os
import shutil
import glob
import llnl.util.tty as tty
@ -36,8 +37,9 @@ class Bcl2fastq2(Package):
call (BCL) files from a sequencing run into FASTQ
files."""
homepage = "https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-18.html"
homepage = "https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html"
version('2.20.0.422', '4dc99f1af208498b7279b66556329488')
version('2.19.1.403', 'baba7a02767fd868e87cb36781d2be26')
version('2.18.0.12', 'fbe06492117f65609c41be0c27e3215c')
# 2.17.1.14 is no longer distributed. If you have a copy of the
@ -65,12 +67,11 @@ class Bcl2fastq2(Package):
# v2.19.1.403 is only available via ftp.
# who knows what the future will hold.
def url_for_version(self, version):
url = "ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/bcl2fastq2-v{0}-tar.zip"
if version.string == '2.19.1.403':
return "ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/bcl2fastq2-v2.19.1-tar.zip"
return url.format(version.up_to(3).dotted)
else:
url = "https://support.illumina.com/content/dam/illumina-support/documents/downloads/software/bcl2fastq/bcl2fastq2-v{0}-tar.zip"
# - required to change the version from dots to dashes.
return url.format(version.dashed)
return url.format(version.up_to(3).dashed)
# Illumina tucks the source inside a gzipped tarball inside a zip
# file. We let the normal Spack expansion bit unzip the zip file,
@ -91,12 +92,12 @@ def wrap():
else:
tty.msg("Unpacking bcl2fastq2 tarball")
tty.msg("cwd sez: {0}".format(os.getcwd()))
tarball = 'bcl2fastq2-v{0}.tar.gz'.format(
self.version.dotted)
shutil.move(join_path('spack-expanded-archive', tarball),
'.')
tarball = glob.glob(join_path('spack-expanded-archive',
'bcl2fastq2*.tar.gz'))[0]
shutil.move(tarball, '.')
os.rmdir('spack-expanded-archive')
tar = which('tar')
tarball = os.path.basename(tarball)
tar('-xf', tarball)
tty.msg("Finished unpacking bcl2fastq2 tarball")
return wrap