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commit: 39736ebd797835df74a7c9dfee1d39bdcf4e7baf |
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Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Mon Apr 27 13:03:43 2015 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Mon Apr 27 13:03:43 2015 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=39736ebd |
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|
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sci-biology/transdecoder: more ebuild cleanup |
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|
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Package-Manager: portage-2.2.18 |
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|
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sci-biology/transdecoder/ChangeLog | 4 ++++ |
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sci-biology/transdecoder/transdecoder-2.0.1.ebuild | 23 ++++++++++++++++++---- |
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2 files changed, 23 insertions(+), 4 deletions(-) |
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|
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diff --git a/sci-biology/transdecoder/ChangeLog b/sci-biology/transdecoder/ChangeLog |
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index fbadc5c..6fd8f5c 100644 |
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--- a/sci-biology/transdecoder/ChangeLog |
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+++ b/sci-biology/transdecoder/ChangeLog |
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@@ -4,6 +4,10 @@ |
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|
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27 Apr 2015; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> |
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transdecoder-2.0.1.ebuild: |
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+ sci-biology/transdecoder: more ebuild cleanup |
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+ |
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+ 27 Apr 2015; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> |
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+ transdecoder-2.0.1.ebuild: |
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sci-biology/transdecoder: ebuild cleanup |
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|
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27 Apr 2015; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> |
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diff --git a/sci-biology/transdecoder/transdecoder-2.0.1.ebuild b/sci-biology/transdecoder/transdecoder-2.0.1.ebuild |
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index 11a7413..e8f5134 100644 |
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--- a/sci-biology/transdecoder/transdecoder-2.0.1.ebuild |
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+++ b/sci-biology/transdecoder/transdecoder-2.0.1.ebuild |
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@@ -18,10 +18,11 @@ IUSE="" |
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|
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DEPEND="" |
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RDEPEND="${DEPEND} |
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- sci-biology/hmmer |
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sci-biology/cd-hit |
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+ sci-biology/hmmer |
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sci-biology/parafly |
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sci-biology/ffindex" |
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+# cdhit-4.6.1 is a real dependency, at least hmmer is optional (also ncbi-tools++ is now used for ORF searches) |
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|
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S="${WORKDIR}"/TransDecoder-2.0.1 |
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@@ -37,10 +38,24 @@ S="${WORKDIR}"/TransDecoder-2.0.1 |
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# you cna get it from http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin |
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|
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src_install(){ |
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- dobin TransDecoder *.pl util/*.pl util/*.sh |
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+ dobin TransDecoder.Predict TransDecoder.LongOrfs |
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+ insinto /usr/share/${PN}/util |
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+ dobin util/*.pl |
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+ # zap the bundled cdhit binaries copied from transdecoder_plugins/cdhit/ to util/bin |
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+ rm -rf util/bin |
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+ # |
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+ # * sci-biology/trinityrnaseq-20140413:0::science |
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+ # * /usr/bin/Fasta_reader.pm |
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+ # * /usr/bin/GFF3_utils.pm |
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+ # * /usr/bin/Gene_obj.pm |
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+ # * /usr/bin/Gene_obj_indexer.pm |
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+ # * /usr/bin/Longest_orf.pm |
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+ # * /usr/bin/Nuc_translator.pm |
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+ # * /usr/bin/TiedHash.pm |
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+ # |
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perl_set_version |
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- insinto ${VENDOR_LIB}/TransDecoder |
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- dobin PerlLib/*.pm |
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+ insinto ${VENDOR_LIB}/${PN} |
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+ dobin PerlLib/*.pm # BUG: install into /usr/bin but wanted to have it readable and executable in ${VENDOR_LIB}/${PN} instead |
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einfo "Fetch on your own:" |
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einfo "wget --mirror -nH -nd http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin" |
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einfo "hmmpress Pfam-AB.hmm.bin" |
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