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authorAndrew Ammerlaan <andrewammerlaan@riseup.net>2021-02-04 06:08:13 +0100
committerAndrew Ammerlaan <andrewammerlaan@riseup.net>2021-02-04 06:08:13 +0100
commit9e1701c4483715ce8127247055278731d33a8079 (patch)
tree527d7e37898bbdd1cb4f481e80f701885a2e1468
parentsci-biology/roche454ace2caf: EAPI bump (diff)
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sci-biology/sailfish: fix configure phase
does not compile at the moment though so no keywords yet Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
-rw-r--r--sci-biology/sailfish/Manifest3
-rw-r--r--sci-biology/sailfish/sailfish-0.10.0.ebuild11
2 files changed, 13 insertions, 1 deletions
diff --git a/sci-biology/sailfish/Manifest b/sci-biology/sailfish/Manifest
index 5b9f831db..025cfe9ea 100644
--- a/sci-biology/sailfish/Manifest
+++ b/sci-biology/sailfish/Manifest
@@ -1,2 +1,5 @@
+DIST jellyfish-2.2.5.tar.gz 1083486 BLAKE2B 545c110199cb2661656ddd558f5ee2b9715a78f6d33275f53aa5a9719247dff4421ef5dd37c3683a3423c8b79ff33395bf4e0ac86cade7480bc604a2b197e214 SHA512 7747030628f82562669c5021aeaca03d8dfc559dc9c3a407e2e4e8de633673f7cf9c60989c16f73deb8e88e7204a3fe84993209a2ebffcb34fd35eac7784e9ab
DIST quasi-mph.zip 414036 BLAKE2B 414ccd806fc11fdc949ecf107db079e4ab0dec8f443f4ba27df9c4273bc3e01f9d4e7c377651a930cf28c77198526a7ed52eb65419a9c29d6cf12a6ecf268b6c SHA512 65d420af549ce138e6d240438919cbfb76a6f137d2767ba45c099c9a946ca04686fedca609a5ebe4c9d371d2587379f35d9e5dd591abe1afc4b7d433bb4f61c9
DIST sailfish-0.10.0.tar.gz 1621862 BLAKE2B d04d8db99e1d191ad1bea690bf43f31d23d6505bc3e80399cfafbbf4e1404edf8a4bbe0532e2c47ec59a5a26f50509342a7143bc0b0c41c3a8723ec0f6e53bd4 SHA512 ec66cff89dac037b84deaf997b7769802f594e69820d42915fb830bfcd527786c9c466a9476bdf2b29b9f7481e98905acf580f4a766765bccaa1b0ced22c4bb2
+DIST sparsehash-2.0.2.tar.gz 321951 BLAKE2B 057776f89fe3ca4b826eec7a142a18106561e4a20eaf907b3996f4dc52f484b84196c3bf9cf6d8bc31bd09aec34fc68b5992560c5fbe8c279c94d18062a96855 SHA512 e086b8beb45f2aa395b5ae49aed8ebaed1cafc9a59ece862f64f067098e2b9c28efc5cfac6b26eea46e5fe6b3db1bfa1afc0b9656c48adc01c3c3d05a5b327e8
+DIST v1.0.tar.gz 86404 BLAKE2B ce59ff034cbd70a504ed8c2e42e552489cc07a80a7130149234294aa2c75329f15ff5c4da4709a40712e18762e160355de67f4f68810856f8bc8218ceffb671d SHA512 ba4b395374da16f9ac22dd3cbf96ab5a67ab4d64a312f382ace883633199bbbd5f7602abe768ac84f6ddf2611eaf2db3d402893bd5dad135d598b4b9853ccd6b
diff --git a/sci-biology/sailfish/sailfish-0.10.0.ebuild b/sci-biology/sailfish/sailfish-0.10.0.ebuild
index 4aef4312e..8ba4d0cf7 100644
--- a/sci-biology/sailfish/sailfish-0.10.0.ebuild
+++ b/sci-biology/sailfish/sailfish-0.10.0.ebuild
@@ -8,7 +8,11 @@ inherit cmake multilib
DESCRIPTION="Rapid Mapping-based Isoform Quantification from RNA-Seq Reads"
HOMEPAGE="https://www.cs.cmu.edu/~ckingsf/software/sailfish/"
SRC_URI="https://github.com/kingsfordgroup/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
- https://github.com/COMBINE-lab/RapMap/archive/quasi-mph.zip"
+ https://github.com/COMBINE-lab/RapMap/archive/quasi-mph.zip
+ https://github.com/gmarcais/Jellyfish/releases/download/v2.2.5/jellyfish-2.2.5.tar.gz
+ https://github.com/COMBINE-lab/sparsehash/archive/sparsehash-2.0.2.tar.gz
+ https://github.com/Kingsford-Group/libgff/archive/v1.0.tar.gz
+"
LICENSE="GPL-3+"
SLOT="0"
@@ -45,10 +49,15 @@ src_unpack() {
mkdir -p "${S}/external"
cp "${DISTDIR}/quasi-mph.zip" "${S}/external/rapmap.zip" || die
mv "${WORKDIR}/RapMap-quasi-mph" "${S}/external/RapMap" || die
+ mv "${WORKDIR}/jellyfish-2.2.5" "${S}/external/jellyfish-2.2.5" || die
+ mv "${WORKDIR}/sparsehash-sparsehash-2.0.2" "${S}/external/sparsehash-sparsehash-2.0.2" || die
+ mv "${WORKDIR}/libgff-1.0" "${S}/external/libgff" || die
mkdir -p "${S}/external/install/lib"
cp "${EPREFIX}/usr/$(get_libdir)/libdivsufsort.so" "${S}/external/install/lib/" || die
cp "${EPREFIX}/usr/$(get_libdir)/libdivsufsort64.so" "${S}/external/install/lib/" || die
cp "${EPREFIX}/usr/$(get_libdir)/libjellyfish-2.0.so" "${S}/external/install/lib/" || die
+ mkdir -p "${S}/external/install/src/rapmap"
+ cp "${S}/external/RapMap/src/"* "${S}/external/install/src/rapmap" || die
}
src_prepare() {