hlrs-software-stack/spack
7
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity

bcl2fastq2: package update (#7794)

Browse source 
* 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
Show stats Download patch file Download diff file Expand all files Collapse all files

19
var/spack/repos/builtin/packages/bcl2fastq2/package.py
View file

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