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-rw-r--r--profiles/package.mask1
-rw-r--r--sci-biology/mRNAmarkup/Manifest3
-rw-r--r--sci-biology/mRNAmarkup/mRNAmarkup-1.0.ebuild57
-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