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| author | Levi Baber <baberlevi@gmail.com> | 2018-11-06 08:36:47 -0600 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2018-11-06 08:36:47 -0600 |
| commit | 4ba3c81bc84a7cacbd3a8d159b22eacc031baca9 (patch) | |
| tree | 371e65c34ffa03ff24fcc0ad94dea31df2cf4836 | |
| parent | d5327d8d4bfa0fd1094dacbdc07a83ed41e4a50e (diff) | |
| download | spack-4ba3c81bc84a7cacbd3a8d159b22eacc031baca9.tar.gz spack-4ba3c81bc84a7cacbd3a8d159b22eacc031baca9.tar.bz2 spack-4ba3c81bc84a7cacbd3a8d159b22eacc031baca9.tar.xz spack-4ba3c81bc84a7cacbd3a8d159b22eacc031baca9.zip | |
snpeff: add wrapper for SnpSift.jar (#9674)
| -rw-r--r-- | var/spack/repos/builtin/packages/snpeff/SnpSift.sh | 3 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/snpeff/package.py | 32 |
2 files changed, 21 insertions, 14 deletions
diff --git a/var/spack/repos/builtin/packages/snpeff/SnpSift.sh b/var/spack/repos/builtin/packages/snpeff/SnpSift.sh new file mode 100644 index 0000000000..3422a77914 --- /dev/null +++ b/var/spack/repos/builtin/packages/snpeff/SnpSift.sh @@ -0,0 +1,3 @@ +#!/bin/sh +# convenience wrapper for the SnpSift jar file +java -jar SnpSift.jar "$@" diff --git a/var/spack/repos/builtin/packages/snpeff/package.py b/var/spack/repos/builtin/packages/snpeff/package.py index 046ad49e52..81e7147d20 100644 --- a/var/spack/repos/builtin/packages/snpeff/package.py +++ b/var/spack/repos/builtin/packages/snpeff/package.py @@ -22,17 +22,21 @@ class Snpeff(Package): def install(self, spec, prefix): install_tree('snpEff', prefix.bin) - # Set up a helper script to call java on the jar file, - # explicitly codes the path for java and the jar file. - script_sh = join_path(os.path.dirname(__file__), "snpEff.sh") - script = prefix.bin.snpEff - install(script_sh, script) - set_executable(script) - - # Munge the helper script to explicitly point to java and the - # jar file. - java = self.spec['java'].prefix.bin.java - kwargs = {'backup': False} - filter_file('^java', java, script, **kwargs) - filter_file('snpEff.jar', join_path(prefix.bin, 'snpEff.jar'), - script, **kwargs) + # Set up a helper script to call java on the jar files, + # explicitly codes the path for java and the jar files. + scripts = ['snpEff', 'SnpSift'] + + for script in scripts: + script_sh = join_path(os.path.dirname(__file__), script + ".sh") + script_path = join_path(prefix.bin, script) + install(script_sh, script_path) + set_executable(script_path) + + # Munge the helper script to explicitly point to java and the + # jar file. + java = self.spec['java'].prefix.bin.java + kwargs = {'backup': False} + filter_file('^java', java, script_path, **kwargs) + filter_file(script + '.jar', + join_path(prefix.bin, script + '.jar'), + script_path, **kwargs) |