diff options
| author | Matteo Guglielmi <matteo.guglielmi@gmail.com> | 2018-04-18 17:11:44 +0200 |
|---|---|---|
| committer | Adam J. Stewart <ajstewart426@gmail.com> | 2018-04-18 10:11:44 -0500 |
| commit | 247f24e0158c78d7c67924a7517fa68f6b034047 (patch) | |
| tree | 83d798653dcfe3f12b5c21da8bfc36b6b8ce71f2 /var | |
| parent | 87747b888f54522c333705ad25c1611982732a29 (diff) | |
| download | spack-247f24e0158c78d7c67924a7517fa68f6b034047.tar.gz spack-247f24e0158c78d7c67924a7517fa68f6b034047.tar.bz2 spack-247f24e0158c78d7c67924a7517fa68f6b034047.tar.xz spack-247f24e0158c78d7c67924a7517fa68f6b034047.zip | |
bcl2fastq2: package update (#7794)
* bcl2fastq2: package update
* package/bcl2fastq2: homepage fix
* package/bcl2fastq2: glob fix
* package/bcl2fastq2: code clean up
* package/bcl2fastq2: code clean up #2
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/bcl2fastq2/package.py | 19 |
1 files changed, 10 insertions, 9 deletions
diff --git a/var/spack/repos/builtin/packages/bcl2fastq2/package.py b/var/spack/repos/builtin/packages/bcl2fastq2/package.py index 5655a8462b..b6e476b55c 100644 --- a/var/spack/repos/builtin/packages/bcl2fastq2/package.py +++ b/var/spack/repos/builtin/packages/bcl2fastq2/package.py @@ -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 @@ class Bcl2fastq2(Package): 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 |