{bio} [goolf-1.4.10] PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb (REVIEW) #2437
{bio} [goolf-1.4.10] PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb (REVIEW) #2437boegel merged 2 commits intoeasybuilders:developfrom
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Easyconfigs unit test suite PASSed (see https://jenkins1.ugent.be/job/easybuild-easyconfigs-pr-builder/5932/console for more details). This pull request is now ready for review/testing. Please try and find someone who can tackle this; contact @boegel if you're not sure what to do. |
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It looks OK to me. I'll try to test it. |
| version = '0.20.4' | ||
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| homepage = 'http://prinseq.sourceforge.net' | ||
| description = """ A bioinformatics tool to PRe-process and show INformation of SEQuence data. """ |
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drop whitespace before and after
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I'd prefer if it got merged with a newer compiler option too (1.7.20 or a foss option). |
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Test report by @boegel |
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| postinstallcmds = ["sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl", # fix shebang line | ||
| "chmod +x %(installdir)s/*.pl"] # add execution permission |
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please format like:
postinstallcmds = [
"sed ...", # fix shebang line
"chmod ...", # add execution permisson
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This actually needs to be moved to the generic Perl extension block. The Python one implements patching wrong shebangs.
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Please open an issue on that in the easyblocks repo?
Or submit a PR for it. ;-)
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Easyconfigs unit test suite PASSed (see https://jenkins1.ugent.be/job/easybuild-easyconfigs-pr-builder/5945/console for more details). This pull request is now ready for review/testing. Please try and find someone who can tackle this; contact @boegel if you're not sure what to do. |
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Test report by @boegel |
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Good to go (moving the |
{bio} [goolf-1.4.10] PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb (REVIEW)
This application is the typical bioinformatics perl script which depends on many extra perl libraries. How I was managing this kind of installation before was adding the perl libraries dependencies to my main Perl easyconfig. This was leading to a really huge list of libraries / extensions in my main perl easyconfig. Inspired by the bundle easyblock I tried this weird easyconfig which uses the tarball easyblock with extra perl extensions to try to keep the perl script and it's dependencies more self-contained.
I am curious to listen @boegel complains :P Do you have any suggestion about a better approach?
I think this can be useful for people deploying bioinfo stuff where this kind of perl applications are quite common CC: @fgeorgatos @pforai @cfenoy @rjeschmi @georg-rath