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