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| author |   Andrew Ammerlaan <andrewammerlaan@riseup.net> | 2021-01-19 12:06:34 +0100 |
|---|---|---|
| committer | Andrew Ammerlaan <andrewammerlaan@riseup.net> | 2021-01-19 12:06:47 +0100 |
| commit | 0069fa855baffaac7a79f53467dc8258eaaa5883 (patch) | |
| tree | 1f025c7aa8c237f91f863fb1829f642275ed492a | |
| parent | sci-biology/mrsfast: fix fetch, version bump (diff) | |
| download | sci-0069fa855baffaac7a79f53467dc8258eaaa5883.tar.gz sci-0069fa855baffaac7a79f53467dc8258eaaa5883.tar.bz2 sci-0069fa855baffaac7a79f53467dc8258eaaa5883.zip | |
sci-biology/mRNAmarkup: version bump, fix fetch
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
| -rw-r--r-- | profiles/package.mask | 1 | ||||
| -rw-r--r-- | sci-biology/mRNAmarkup/Manifest | 3 | ||||
| -rw-r--r-- | sci-biology/mRNAmarkup/mRNAmarkup-1.0.ebuild | 57 | ||||
| -rw-r--r-- | sci-biology/mRNAmarkup/mRNAmarkup-5.21.2019.ebuild (renamed from sci-biology/mRNAmarkup/mRNAmarkup-1.1.ebuild) | 12 |
4 files changed, 6 insertions, 67 deletions
diff --git a/profiles/package.mask b/profiles/package.mask index 650fb6a4b..43fa4e9d6 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -86,4 +86,3 @@ sci-biology/mavid sci-biology/MeV sci-biology/MolBioLib sci-biology/mreps -sci-biology/mRNAmarkup diff --git a/sci-biology/mRNAmarkup/Manifest b/sci-biology/mRNAmarkup/Manifest index f14ab8b9e..fb61347b3 100644 --- a/sci-biology/mRNAmarkup/Manifest +++ b/sci-biology/mRNAmarkup/Manifest @@ -1,2 +1 @@ -DIST mRNAmarkup-10-3-2013.tar.gz 225283371 SHA256 4fce294745dde0e55c0dda71c9c186d2372c28850d26cc7f4db68b23278f84a1 SHA512 bf752ed2459bb01ddb6d982a7aee4417634a52c42be5eda56f680aaf77e5e37c6feb3199f03784e754d95a417b9cda3eff83e47c31a733365f25e93a4c412303 WHIRLPOOL a3905f30aeda2980b803a50734529d4eca8b216398eb6db1b9d38bc372b5470971e50b87cfffa59c7d84c64333c5b6422facbe4574947f2f170ad28291b31f14 -DIST mRNAmarkup-4-8-2015.tar.gz 192523324 BLAKE2B 5a327c1cef195bb637eb5cf22f030f1e18c4a7374630dee0f777e68b86888b558a07766aef374c9c1373154ad04e728c105c803372707321c0ec0cabae55f143 SHA512 caf537f98bf3a11e28e47a6e6833eb70e1f810cd1ad3033d30f7a941fb136f08e243abb373a105a86191ba939fc56537967ef598f714d1a8f40f6ee9967732b3 +DIST mRNAmarkup-5-21-2019.tar.gz 192535480 BLAKE2B 5aa385ddae79f2d18649ab70ac2939a478714abd84a59621d852888e9f7df4fd666baea8b8e905756a0f259471a35c6ca1fb5f7c2fa7a50769b4cf7c32dd431b SHA512 c05b685db7992e6278b56b34ad4e77c1f1c4bfb5b9f4880062fa07b5674272e5b950480bbfdd5cbfc037e6b87c10544d0fc67a8b55370037649203ce1c730d2a diff --git a/sci-biology/mRNAmarkup/mRNAmarkup-1.0.ebuild b/sci-biology/mRNAmarkup/mRNAmarkup-1.0.ebuild deleted file mode 100644 index dbdc3e368..000000000 --- a/sci-biology/mRNAmarkup/mRNAmarkup-1.0.ebuild +++ /dev/null @@ -1,57 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -DESCRIPTION="Transcript annotation workflow" -HOMEPAGE="http://brendelgroup.org/bioinformatics2go/mRNAmarkup.php" -SRC_URI="http://www.brendelgroup.org/bioinformatics2go/Download/mRNAmarkup-10-3-2013.tar.gz" # 215MB - -# 0README in version 20131003 says it is 1.0 - -LICENSE="mRNAmarkup" -SLOT="0" -KEYWORDS="~amd64" -IUSE="" - -DEPEND=" - sci-biology/ncbi-tools++ - sci-biology/estscan" -# sci-biology/MuSeqBox has fetch-restrict and probably only works with old BLAST plaintex output -# but, mRNAmarkup/INSTALL says: -# 'For convenience, a copy of the MuSeqBox code distribution is included in directory src/contributed -# -# has a slightly modified estscan copy in src/contributed -RDEPEND="${DEPEND}" - -S="${WORKDIR}"/"${PN}" - -src_prepare(){ - sed -e \ - "s#configfile=$installdir/mRNAmarkup.conf#configfile=/usr/share/mRNAmarkup/etc/mRNAmarkup.conf#" \ - -i bin/mRNAmarkup.orig || die - sed -e \ - "s#$installdir/bin/ESTScan.conf#/usr/share/mRNAmarkup/etc/ESTScan.conf#" \ - -i bin/mRNAmarkup.orig -} - -src_compile(){ - cd src - emake -} - -src_install(){ - mv bin/mRNAmarkup.orig bin/mRNAmarkup - sed -e 's#INSTALLDIR#/usr/share/mRNAmarkup/etc/#' -i bin/mRNAmarkup - dobin bin/mRNAmarkup bin/*.pl bin/dnatopro bin/genestat - # TODO: there are some more files in bin/ , sigh! - insinto /usr/share/mRNAmarkup/etc - mv mRNAmarkup.conf.orig mRNAmarkup.conf - doins mRNAmarkup.conf - doins bin/ESTScan.conf - dodoc 0README INSTALL -} - -pkg_postinst(){ - einfo "Please obtain a local copy of NCBI CDD dastabase" -} diff --git a/sci-biology/mRNAmarkup/mRNAmarkup-1.1.ebuild b/sci-biology/mRNAmarkup/mRNAmarkup-5.21.2019.ebuild index f68f0d335..fb37b69f9 100644 --- a/sci-biology/mRNAmarkup/mRNAmarkup-1.1.ebuild +++ b/sci-biology/mRNAmarkup/mRNAmarkup-5.21.2019.ebuild @@ -1,18 +1,15 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 DESCRIPTION="Transcript annotation workflow" HOMEPAGE="http://brendelgroup.org/bioinformatics2go/mRNAmarkup.php" -SRC_URI="http://www.brendelgroup.org/bioinformatics2go/Download/mRNAmarkup-4-8-2015.tar.gz" # 184MB - -# mRNAmarkup-4-8-2015.tar.gz is 1.1 version +SRC_URI="http://www.brendelgroup.org/bioinformatics2go/Download/mRNAmarkup-${PV//./-}.tar.gz" # 184MB LICENSE="mRNAmarkup" SLOT="0" KEYWORDS="~amd64" -IUSE="" DEPEND=" sci-biology/ncbi-tools++ @@ -24,9 +21,10 @@ DEPEND=" # has a slightly modified estscan copy in src/contributed RDEPEND="${DEPEND}" -S="${WORKDIR}"/"${PN}" +S="${WORKDIR}/${PN}" src_prepare(){ + default sed -e \ "s#configfile=$installdir/mRNAmarkup.conf#configfile=/usr/share/mRNAmarkup/etc/mRNAmarkup.conf#" \ -i bin/mRNAmarkup.orig || die |