diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/fastq-screen/package.py | 27 |
1 files changed, 21 insertions, 6 deletions
diff --git a/var/spack/repos/builtin/packages/fastq-screen/package.py b/var/spack/repos/builtin/packages/fastq-screen/package.py index 2f5fbb2074..4d9acde2c9 100644 --- a/var/spack/repos/builtin/packages/fastq-screen/package.py +++ b/var/spack/repos/builtin/packages/fastq-screen/package.py @@ -12,16 +12,31 @@ class FastqScreen(Package): the library matches with what you expect.""" homepage = "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/" - url = "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/fastq_screen_v0.11.2.tar.gz" + url = "https://github.com/StevenWingett/FastQ-Screen/archive/refs/tags/v0.15.3.tar.gz" - version("0.11.2", sha256="a179df1f5803b42bbbb2b50af05ea18ae6fefcbf7020ca2feeb0d3c598a65207") + version("0.15.3", sha256="002750d78ca50fe0f789e24445e10988e16244f81b4f0189bf2fc4ee8b680be5") + version( + "0.11.2", + sha256="a179df1f5803b42bbbb2b50af05ea18ae6fefcbf7020ca2feeb0d3c598a65207", + url="https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/fastq_screen_v0.11.2.tar.gz", + ) + variant("bismark", default=False, description="Enable bisulfite mapping with bismark") + variant("bowtie", default=False, description="Enable mapping with bowtie") + variant("bwa", default=False, description="Enable mapping with bwa") + + # general dependencies depends_on("perl", type="run") depends_on("perl-gdgraph", type="run") - depends_on("bowtie") - depends_on("bowtie2") - depends_on("bwa") - depends_on("samtools") + depends_on("bowtie2", type="run") + depends_on("samtools", type="run") + # variant dependencies + depends_on("bismark", type="run", when="+bismark") + depends_on("bowtie", type="run", when="+bowtie") + depends_on("bwa", type="run", when="+bwa") + + def patch(self): + filter_file("/usr/bin/perl", self.spec["perl"].command.path, "fastq_screen", backup=False) def install(self, spec, prefix): install_tree(".", prefix.bin) |