diff options
Diffstat (limited to 'sci-biology/embassy-hmmer')
3 files changed, 124 insertions, 0 deletions
diff --git a/sci-biology/embassy-hmmer/Manifest b/sci-biology/embassy-hmmer/Manifest index cfef1c3b4a7b..6b9ca2ab9873 100644 --- a/sci-biology/embassy-hmmer/Manifest +++ b/sci-biology/embassy-hmmer/Manifest @@ -1 +1,2 @@ DIST embassy-hmmer-2.3.2.650.tar.gz 587775 SHA256 1464ff5e87c7c429f2fc78ac3554f8bd32cdaf49b8bed095fce6268b9afd4f6a SHA512 eb2c037fec70f4113b9ab59cc4eca9a608e8d0971a7bcc4612d60b1e28556444dd3ecdea4ff7b8f8b34711ad9f655334857e7510e89060459c81994a3abcc02a WHIRLPOOL 59027e96d3e629eb771fa966be95cd30138d6b97223056c95c1cc19d21ec0ffe555ff12f2cadc372ea303a0e06a9c1e673c4e32b2a50d8fd2ab2071d2c04cb83 +DIST embassy-hmmer-2.3.2.660.tar.gz 587775 SHA256 1464ff5e87c7c429f2fc78ac3554f8bd32cdaf49b8bed095fce6268b9afd4f6a SHA512 eb2c037fec70f4113b9ab59cc4eca9a608e8d0971a7bcc4612d60b1e28556444dd3ecdea4ff7b8f8b34711ad9f655334857e7510e89060459c81994a3abcc02a WHIRLPOOL 59027e96d3e629eb771fa966be95cd30138d6b97223056c95c1cc19d21ec0ffe555ff12f2cadc372ea303a0e06a9c1e673c4e32b2a50d8fd2ab2071d2c04cb83 diff --git a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.660.ebuild b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.660.ebuild new file mode 100644 index 000000000000..7db8bf9ed7b9 --- /dev/null +++ b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.660.ebuild @@ -0,0 +1,22 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +EBO_DESCRIPTION="HMMER wrapper - sequence analysis with profile HMMs" + +EBO_EAUTORECONF=1 + +inherit emboss-r2 + +KEYWORDS="~amd64 ~x86 ~x86-linux" + +RDEPEND="sci-biology/hmmer:2" + +S="${WORKDIR}/HMMER-2.3.2.650" +PATCHES=( + "${FILESDIR}"/${PN}-2.3.2.650_fix-build-system.patch + # sci-biology/hmmer:2 has renamed commandline program names + "${FILESDIR}"/${PN}-2.3.2.660-slotted-hmmer2.patch +) diff --git a/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.660-slotted-hmmer2.patch b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.660-slotted-hmmer2.patch new file mode 100644 index 000000000000..f202ddf3d0b5 --- /dev/null +++ b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.660-slotted-hmmer2.patch @@ -0,0 +1,101 @@ +Amend command-line names for Gentoo SLOTed hmmer:2 + +--- a/src/ehmmalign.c ++++ b/src/ehmmalign.c +@@ -99,7 +99,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajFmtPrintS(&cmd, "%S ", ajAcdGetpathC("hmmalign")); ++ ajFmtPrintS(&cmd, "%S ", ajAcdGetpathC("hmmalign2")); + if(mapali) + ajFmtPrintAppS(&cmd, " --mapali %s ", ajFileGetNameC(mapali)); + if(withali) +--- a/src/ehmmbuild.c ++++ b/src/ehmmbuild.c +@@ -146,7 +146,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajStrAssignS(&cmd, ajAcdGetpathC("hmmbuild")); ++ ajStrAssignS(&cmd, ajAcdGetpathC("hmmbuild2")); + if(prior) + ajFmtPrintAppS(&cmd, " --prior %s ", ajFileGetNameC(prior)); + if(null) +--- a/src/ehmmcalibrate.c ++++ b/src/ehmmcalibrate.c +@@ -98,7 +98,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajStrAssignS(&cmd, ajAcdGetpathC("hmmcalibrate")); ++ ajStrAssignS(&cmd, ajAcdGetpathC("hmmcalibrate2")); + if(cpu) + ajFmtPrintAppS(&cmd, " --cpu %d ", cpu); + if(fixed) +--- a/src/ehmmconvert.c ++++ b/src/ehmmconvert.c +@@ -72,7 +72,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajStrAssignS(&cmd, ajAcdGetpathC("hmmconvert")); ++ ajStrAssignS(&cmd, ajAcdGetpathC("hmmconvert2")); + + /* ACD option only allows one selection */ + option = ajStrGetCharFirst(format); +--- a/src/ehmmemit.c ++++ b/src/ehmmemit.c +@@ -79,7 +79,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajStrAssignS(&cmd, ajAcdGetpathC("hmmemit")); ++ ajStrAssignS(&cmd, ajAcdGetpathC("hmmemit2")); + ajFmtPrintAppS(&cmd, " --seed %d ", seed); + if(a) + ajStrAppendC(&cmd, " -a "); +--- a/src/ehmmfetch.c ++++ b/src/ehmmfetch.c +@@ -74,7 +74,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajStrAssignS(&cmd, ajAcdGetpathC("hmmfetch")); ++ ajStrAssignS(&cmd, ajAcdGetpathC("hmmfetch2")); + if(nhmm) + ajStrAppendC(&cmd, " -n "); + /* Note the output redirected to outfname */ +--- a/src/ehmmindex.c ++++ b/src/ehmmindex.c +@@ -68,7 +68,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajFmtPrintS(&cmd, "%S ", ajAcdGetpathC("hmmindex")); ++ ajFmtPrintS(&cmd, "%S ", ajAcdGetpathC("hmmindex2")); + ajStrAppendC(&cmd, ajFileGetNameC(database)); + + +--- a/src/ehmmpfam.c ++++ b/src/ehmmpfam.c +@@ -122,7 +122,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajStrAssignS(&cmd, ajAcdGetpathC("hmmpfam")); ++ ajStrAssignS(&cmd, ajAcdGetpathC("hmmpfam2")); + if(nuc) + ajStrAppendC(&cmd, " -n "); + ajFmtPrintAppS(&cmd, " -A %d -E %f -T %f -Z %d", A, E, T, Z); +--- a/src/ehmmsearch.c ++++ b/src/ehmmsearch.c +@@ -102,7 +102,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajStrAssignS(&cmd, ajAcdGetpathC("hmmsearch")); ++ ajStrAssignS(&cmd, ajAcdGetpathC("hmmsearch2")); + ajFmtPrintAppS(&cmd, " -A %d -E %f -T %f -Z %d", A, E, T, Z); + if(compat) + ajStrAppendC(&cmd, " --compat "); |