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commit: c0a145c569b658ac97b0addecdee386768d4bb16 |
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Author: David Seifert <soap <AT> gentoo <DOT> org> |
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AuthorDate: Sun Oct 9 12:44:16 2016 +0000 |
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Commit: David Seifert <soap <AT> gentoo <DOT> org> |
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CommitDate: Sun Oct 9 15:14:18 2016 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c0a145c5 |
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|
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sci-biology/hmmer: Version bump to 3.1_beta2 |
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|
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* EAPI=6 |
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* Make perl shebangs portable |
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* Install headers into 'hmmer3' subdir |
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|
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Package-Manager: portage-2.3.1 |
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|
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sci-biology/hmmer/Manifest | 1 + |
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.../hmmer-3.1_beta2-fix-header-install-path.patch | 89 ++++++ |
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.../files/hmmer-3.1_beta2-fix-perl-shebangs.patch | 331 +++++++++++++++++++++ |
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sci-biology/hmmer/hmmer-3.1_beta2.ebuild | 49 +++ |
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4 files changed, 470 insertions(+) |
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|
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diff --git a/sci-biology/hmmer/Manifest b/sci-biology/hmmer/Manifest |
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index 7fef69f..dada007 100644 |
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--- a/sci-biology/hmmer/Manifest |
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+++ b/sci-biology/hmmer/Manifest |
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@@ -1,2 +1,3 @@ |
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DIST hmmer-2.3.2.tar.gz 1024933 SHA256 d20e1779fcdff34ab4e986ea74a6c4ac5c5f01da2993b14e92c94d2f076828b4 SHA512 5abf9c304de38b183a5beab7a5cfc75c3774ff6e161b7b8e55a0eae9fd156dbb7ed95d216c16d3c585c494bb69e3a9fdfabfb5dc729b7050a4d1be95c74df7d7 WHIRLPOOL 604cc3f532d6eae3fbca893d991d0714a5a897fbac3059d63fdbebc6221e9321c2b444db2700e7068a11c043c0a7f9f3935617a3aa1878ca06ba18c558d55d40 |
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DIST hmmer-3.0.tar.gz 3952015 SHA256 6977e6473fcb554b1d5a86dc9edffffa53918c1bd88d7fd20d7499f1ba719e83 SHA512 752f06b0494a87ccd2cf6aa93e622fd02173eaa0df60df0527b3361dcaa2baf2b45a2daf0123217c0029bc9d95e505a92f1e97039eb8b7218b4c4b65ddad1db5 WHIRLPOOL a181ce8ddb016bf1209c83fa754163e9ac653acb51fed13dee8598565d2f058a118fca04229aef7e4e5a79aae86712639b8e43bf7e12c50a8bf22e32be9df658 |
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+DIST hmmer-3.1b2.tar.gz 5965253 SHA256 dd16edf4385c1df072c9e2f58c16ee1872d855a018a2ee6894205277017b5536 SHA512 64c8a840cb62160a1c13a20e64f42d297edb7969425d5047eefd8ee9f992d66612d62843523e8f33a2c38568ce1b0a9df23dd1d3ecf6773007f6db12d4cc4771 WHIRLPOOL 0b6d17b5f5efe31873cde93ff33cc5b01c53de8e1daf1ed473ef92d6585f34abcbb31e35e4d02537fbbc2c808131b70a0f51a3832ee332e23246cbc75edc354a |
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|
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diff --git a/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-header-install-path.patch b/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-header-install-path.patch |
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new file mode 100644 |
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index 00000000..b9ff5b9 |
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--- /dev/null |
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+++ b/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-header-install-path.patch |
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@@ -0,0 +1,89 @@ |
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+Install headers into 'hmmer3' subdir and not into global includedir. |
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+ |
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+--- a/easel/Makefile.in |
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++++ b/easel/Makefile.in |
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+@@ -465,11 +465,12 @@ |
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+ ${INSTALL} -d ${DESTDIR}${bindir} |
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+ ${INSTALL} -d ${DESTDIR}${libdir} |
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+ ${INSTALL} -d ${DESTDIR}${includedir} |
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++ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3 |
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+ ${INSTALL} -m 0644 libeasel.a ${DESTDIR}${libdir}/ |
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+ for file in ${HDRS}; do\ |
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+- ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\ |
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++ ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\ |
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+ done |
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+- ${INSTALL} -m 0644 esl_config.h ${DESTDIR}${includedir}/ |
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++ ${INSTALL} -m 0644 esl_config.h ${DESTDIR}${includedir}/hmmer3/ |
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+ ${QUIET_SUBDIR0}miniapps ${QUIET_SUBDIR1} install |
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+ |
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+ # "make uninstall" reverses the steps of "make install" |
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+--- a/Makefile.in |
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++++ b/Makefile.in |
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+@@ -143,6 +143,7 @@ |
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+ ${INSTALL} -d ${DESTDIR}${bindir} |
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+ ${INSTALL} -d ${DESTDIR}${libdir} |
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+ ${INSTALL} -d ${DESTDIR}${includedir} |
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++ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3 |
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+ ${INSTALL} -d ${DESTDIR}${man1dir} |
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+ ${INSTALL} -d ${DESTDIR}${pdfdir} |
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+ ${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} install |
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+--- a/src/impl_dummy/Makefile.in |
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++++ b/src/impl_dummy/Makefile.in |
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+@@ -152,8 +152,9 @@ |
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+ ${CC} ${CFLAGS} ${SIMDFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS} |
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+ |
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+ install: |
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++ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3 |
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+ for file in ${HDRS}; do \ |
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+- ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\ |
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++ ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\ |
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+ done |
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+ |
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+ uninstall: |
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+--- a/src/impl_sse/Makefile.in |
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++++ b/src/impl_sse/Makefile.in |
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+@@ -155,8 +155,9 @@ |
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+ |
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+ |
84 |
+ install: |
85 |
++ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3 |
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+ for file in ${HDRS}; do \ |
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+- ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\ |
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++ ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\ |
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+ done |
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+ |
91 |
+ uninstall: |
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+--- a/src/impl_vmx/Makefile.in |
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++++ b/src/impl_vmx/Makefile.in |
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+@@ -152,8 +152,9 @@ |
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+ ${CC} ${CFLAGS} ${SIMDFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS} |
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+ |
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+ install: |
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++ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3 |
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+ for file in ${HDRS}; do \ |
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+- ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\ |
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++ ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\ |
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+ done |
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+ |
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+ uninstall: |
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+--- a/src/Makefile.in |
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++++ b/src/Makefile.in |
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+@@ -322,15 +322,16 @@ |
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+ ${CC} ${CFLAGS} ${SIMDFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS} |
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+ |
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+ install: |
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++ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3 |
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+ ${QUIET_SUBDIR0}${IMPLDIR} ${QUIET_SUBDIR1} install |
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+ for file in ${PROGS}; do \ |
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+ ${INSTALL} -m 0755 $$file ${DESTDIR}${bindir}/ ;\ |
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+ done |
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+ ${INSTALL} -m 0755 libhmmer.a ${DESTDIR}${libdir}/ |
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+ for file in ${HDRS}; do \ |
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+- ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\ |
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++ ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\ |
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+ done |
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+- ${INSTALL} -m 0644 p7_config.h ${DESTDIR}${includedir}/ ;\ |
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++ ${INSTALL} -m 0644 p7_config.h ${DESTDIR}${includedir}/hmmer3/ ;\ |
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+ |
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+ uninstall: |
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+ ${QUIET_SUBDIR0}${IMPLDIR} ${QUIET_SUBDIR1} uninstall |
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|
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diff --git a/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-perl-shebangs.patch b/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-perl-shebangs.patch |
128 |
new file mode 100644 |
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index 00000000..39fdbd5 |
130 |
--- /dev/null |
131 |
+++ b/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-perl-shebangs.patch |
132 |
@@ -0,0 +1,331 @@ |
133 |
+Fix perl shebangs to be portable and usable on Prefix. |
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+See also: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/ |
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+ |
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+--- a/easel/demotic/infernal_tab2gff.pl |
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++++ b/easel/demotic/infernal_tab2gff.pl |
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+@@ -1,4 +1,4 @@ |
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+-#!/usr/bin/perl -w -I/groups/eddy/home/jonest/Demotic |
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++#!/usr/bin/env perl |
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+ |
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+ # TAJ 6/23/08 last mod 7/10/08 |
143 |
+ # Purpose: flexibly convert "cmsearch --tabfile TAB.out" output to GFF format |
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+--- a/easel/demotic/test.pl |
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++++ b/easel/demotic/test.pl |
146 |
+@@ -1,4 +1,4 @@ |
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+-#! /usr/bin/perl |
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++#!/usr/bin/env perl |
149 |
+ |
150 |
+ use demotic_blast; |
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+ |
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+--- a/easel/devkit/rmanprocess.pl |
153 |
++++ b/easel/devkit/rmanprocess.pl |
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+@@ -1,4 +1,4 @@ |
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+-#! /usr/bin/perl |
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++#!/usr/bin/env perl |
157 |
+ |
158 |
+ # rmanprocess.pl <rman LaTeX2e output> |
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+ # |
160 |
+--- a/easel/miniapps/esl-afetch.itest.pl |
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++++ b/easel/miniapps/esl-afetch.itest.pl |
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+@@ -1,4 +1,4 @@ |
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+-#! /usr/bin/perl |
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++#!/usr/bin/env perl |
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+ |
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+ # Testing the esl-afetch miniapp |
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+ # |
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+--- a/easel/miniapps/esl-alimanip.itest.pl |
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++++ b/easel/miniapps/esl-alimanip.itest.pl |
170 |
+@@ -1,4 +1,4 @@ |
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+-#! /usr/bin/perl |
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++#!/usr/bin/env perl |
173 |
+ |
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+ # Integrated test of the esl-alimanip miniapp. |
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+ # |
176 |
+--- a/easel/miniapps/esl-alimap.itest.pl |
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++++ b/easel/miniapps/esl-alimap.itest.pl |
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+@@ -1,4 +1,4 @@ |
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+-#! /usr/bin/perl |
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++#!/usr/bin/env perl |
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+ |
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+ # Integrated test of the esl-alimap miniapp. |
183 |
+ # |
184 |
+--- a/easel/miniapps/esl-alimask.itest.pl |
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++++ b/easel/miniapps/esl-alimask.itest.pl |
186 |
+@@ -1,4 +1,4 @@ |
187 |
+-#! /usr/bin/perl |
188 |
++#!/usr/bin/env perl |
189 |
+ |
190 |
+ # Integrated test of esl-alimask miniapp. |
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+ # |
192 |
+--- a/easel/miniapps/esl-alimerge.itest.pl |
193 |
++++ b/easel/miniapps/esl-alimerge.itest.pl |
194 |
+@@ -1,4 +1,4 @@ |
195 |
+-#! /usr/bin/perl |
196 |
++#!/usr/bin/env perl |
197 |
+ |
198 |
+ # Integrated test of esl-alimerge miniapp. |
199 |
+ # |
200 |
+--- a/easel/miniapps/esl-alistat.itest.pl |
201 |
++++ b/easel/miniapps/esl-alistat.itest.pl |
202 |
+@@ -1,4 +1,4 @@ |
203 |
+-#! /usr/bin/perl |
204 |
++#!/usr/bin/env perl |
205 |
+ |
206 |
+ # Integrated test of the esl-alistat miniapp. |
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+ # |
208 |
+--- a/easel/miniapps/esl-compalign.itest.pl |
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++++ b/easel/miniapps/esl-compalign.itest.pl |
210 |
+@@ -1,4 +1,4 @@ |
211 |
+-#! /usr/bin/perl |
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++#!/usr/bin/env perl |
213 |
+ |
214 |
+ # Integrated test of the esl-compalign miniapp. |
215 |
+ # |
216 |
+--- a/easel/miniapps/esl-construct.itest.pl |
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++++ b/easel/miniapps/esl-construct.itest.pl |
218 |
+@@ -1,4 +1,4 @@ |
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+-#! /usr/bin/perl |
220 |
++#!/usr/bin/env perl |
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+ |
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+ # Integrated test of the esl-construct miniapp. |
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+ # |
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+--- a/easel/miniapps/esl-mask.itest.pl |
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++++ b/easel/miniapps/esl-mask.itest.pl |
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+@@ -1,4 +1,4 @@ |
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+-#! /usr/bin/perl |
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++#!/usr/bin/env perl |
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+ |
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+ # Integrated test of esl-mask miniapp. |
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+ # |
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+--- a/easel/miniapps/esl-seqrange.itest.pl |
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++++ b/easel/miniapps/esl-seqrange.itest.pl |
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+@@ -1,4 +1,4 @@ |
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+-#! /usr/bin/perl |
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++#!/usr/bin/env perl |
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+ |
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+ # Integrated test of the esl-seqrange miniapp. |
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+ # |
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+--- a/easel/miniapps/esl-shuffle.itest.pl |
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++++ b/easel/miniapps/esl-shuffle.itest.pl |
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+@@ -1,4 +1,4 @@ |
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+-#! /usr/bin/perl |
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++#!/usr/bin/env perl |
245 |
+ |
246 |
+ # Integrated test of esl-shuffle miniapp |
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+ # |
248 |
+--- a/easel/miniapps/esl-ssdraw.itest.pl |
249 |
++++ b/easel/miniapps/esl-ssdraw.itest.pl |
250 |
+@@ -1,4 +1,4 @@ |
251 |
+-#! /usr/bin/perl |
252 |
++#!/usr/bin/env perl |
253 |
+ |
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+ # Integrated test of the esl-ssdraw miniapp. |
255 |
+ # |
256 |
+--- a/easel/testsuite/coverage_report.pl |
257 |
++++ b/easel/testsuite/coverage_report.pl |
258 |
+@@ -1,4 +1,4 @@ |
259 |
+-#! /usr/bin/perl |
260 |
++#!/usr/bin/env perl |
261 |
+ |
262 |
+ # Measures testsuite coverage (as percentage of source lines), |
263 |
+ # using gcov. |
264 |
+--- a/easel/testsuite/driver_report.pl |
265 |
++++ b/easel/testsuite/driver_report.pl |
266 |
+@@ -1,4 +1,4 @@ |
267 |
+-#! /usr/bin/perl |
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++#!/usr/bin/env perl |
269 |
+ |
270 |
+ # Make sure that all drivers compile. |
271 |
+ # (Eventually, we should also make sure they run! But that |
272 |
+--- a/easel/testsuite/i1-degen-residues.pl |
273 |
++++ b/easel/testsuite/i1-degen-residues.pl |
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+@@ -1,4 +1,4 @@ |
275 |
+-#! /usr/bin/perl |
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++#!/usr/bin/env perl |
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+ |
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+ # Integration tests of reading all valid protein sequence residue characters. |
279 |
+ # |
280 |
+--- a/easel/testsuite/i2-ncbi-indices.pl |
281 |
++++ b/easel/testsuite/i2-ncbi-indices.pl |
282 |
+@@ -1,4 +1,4 @@ |
283 |
+-#! /usr/bin/perl |
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++#!/usr/bin/env perl |
285 |
+ |
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+ # Testing that we can read FASTA files, even if they have NCBI |
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+ # formatted BLAST databases in the same directory. |
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+--- a/easel/testsuite/i3-blank-gf.pl |
289 |
++++ b/easel/testsuite/i3-blank-gf.pl |
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+@@ -1,4 +1,4 @@ |
291 |
+-#! /usr/bin/perl |
292 |
++#!/usr/bin/env perl |
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+ |
294 |
+ # Bug #e5: blank text line following #=GF <tag> handled improperly. |
295 |
+ # |
296 |
+--- a/easel/testsuite/valgrind_report.pl |
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++++ b/easel/testsuite/valgrind_report.pl |
298 |
+@@ -1,4 +1,4 @@ |
299 |
+-#! /usr/bin/perl |
300 |
++#!/usr/bin/env perl |
301 |
+ |
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+ # Run the testsuite under Valgrind, to check for memory leakage. |
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+ # |
304 |
+--- a/profmark/pmark-master.pl |
305 |
++++ b/profmark/pmark-master.pl |
306 |
+@@ -1,4 +1,4 @@ |
307 |
+-#! /usr/bin/perl -w |
308 |
++#!/usr/bin/env perl |
309 |
+ |
310 |
+ # The top level script that runs a pmark benchmark. |
311 |
+ # |
312 |
+--- a/profmark/rocplot.pl |
313 |
++++ b/profmark/rocplot.pl |
314 |
+@@ -1,4 +1,4 @@ |
315 |
+-#! /usr/bin/perl |
316 |
++#!/usr/bin/env perl |
317 |
+ |
318 |
+ $nsearches = 2809; |
319 |
+ |
320 |
+--- a/src/hmmpress.itest.pl |
321 |
++++ b/src/hmmpress.itest.pl |
322 |
+@@ -1,4 +1,4 @@ |
323 |
+-#! /usr/bin/perl |
324 |
++#!/usr/bin/env perl |
325 |
+ |
326 |
+ # Integrated test of hmmpress |
327 |
+ # |
328 |
+--- a/testsuite/i10-duplicate-names.pl |
329 |
++++ b/testsuite/i10-duplicate-names.pl |
330 |
+@@ -1,4 +1,4 @@ |
331 |
+-#! /usr/bin/perl |
332 |
++#!/usr/bin/env perl |
333 |
+ |
334 |
+ # Check that we can deal with profiles and sequences that contain |
335 |
+ # duplicate names, both as queries and targets. |
336 |
+--- a/testsuite/i11-hmmalign-mapali.pl |
337 |
++++ b/testsuite/i11-hmmalign-mapali.pl |
338 |
+@@ -1,4 +1,4 @@ |
339 |
+-#! /usr/bin/perl |
340 |
++#!/usr/bin/env perl |
341 |
+ |
342 |
+ # Another test of the hmmalign --mapali option, after Elena reports |
343 |
+ # bug #h73 in bad interaction of checksum calculation and marking |
344 |
+--- a/testsuite/i12-delete-corruption.pl |
345 |
++++ b/testsuite/i12-delete-corruption.pl |
346 |
+@@ -1,4 +1,4 @@ |
347 |
+-#! /usr/bin/perl |
348 |
++#!/usr/bin/env perl |
349 |
+ |
350 |
+ # Bug #h77: hmmalign corrupts column preceding an all-delete column |
351 |
+ # |
352 |
+--- a/testsuite/i13-msa-integrity.pl |
353 |
++++ b/testsuite/i13-msa-integrity.pl |
354 |
+@@ -1,4 +1,4 @@ |
355 |
+-#! /usr/bin/perl |
356 |
++#!/usr/bin/env perl |
357 |
+ |
358 |
+ # Look for any problems in hmmalign that corrupt the input sequences. |
359 |
+ # |
360 |
+--- a/testsuite/i14-hmmemit-consensus.pl |
361 |
++++ b/testsuite/i14-hmmemit-consensus.pl |
362 |
+@@ -1,4 +1,4 @@ |
363 |
+-#! /usr/bin/perl |
364 |
++#!/usr/bin/env perl |
365 |
+ |
366 |
+ # Tests hmmemit -c and hmmemit -C consensus-generating options. |
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+ # |
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+--- a/testsuite/i15-hmmconvert.pl |
369 |
++++ b/testsuite/i15-hmmconvert.pl |
370 |
+@@ -1,4 +1,4 @@ |
371 |
+-#! /usr/bin/perl |
372 |
++#!/usr/bin/env perl |
373 |
+ |
374 |
+ # Bug #h80: hmmconvert can't read H2 Nucleic files |
375 |
+ # |
376 |
+--- a/testsuite/i16-build-allins.pl |
377 |
++++ b/testsuite/i16-build-allins.pl |
378 |
+@@ -1,4 +1,4 @@ |
379 |
+-#! /usr/bin/perl |
380 |
++#!/usr/bin/env perl |
381 |
+ |
382 |
+ # Bug #h82: hmmbuild corrupts resave alignment on all-insert seq |
383 |
+ # |
384 |
+--- a/testsuite/i17-stdin.pl |
385 |
++++ b/testsuite/i17-stdin.pl |
386 |
+@@ -1,4 +1,4 @@ |
387 |
+-#! /usr/bin/perl |
388 |
++#!/usr/bin/env perl |
389 |
+ |
390 |
+ # Test that programs accept and reject argument of '-' (for reading |
391 |
+ # data from stdin, rather than from files) as they're supposed to. |
392 |
+--- a/testsuite/i18-nhmmer-generic.pl |
393 |
++++ b/testsuite/i18-nhmmer-generic.pl |
394 |
+@@ -1,4 +1,4 @@ |
395 |
+-#! /usr/bin/perl |
396 |
++#!/usr/bin/env perl |
397 |
+ |
398 |
+ # Test of hmmbuild/nhmmer as used to build a DNA model, then query a |
399 |
+ # a database of long (1MB). |
400 |
+--- a/testsuite/i19-hmmpgmd-ga.pl |
401 |
++++ b/testsuite/i19-hmmpgmd-ga.pl |
402 |
+@@ -1,4 +1,4 @@ |
403 |
+-#! /usr/bin/perl |
404 |
++#!/usr/bin/env perl |
405 |
+ |
406 |
+ # Test that hmmpgmd is correctly applying bit score thresholds; |
407 |
+ # in this case, the --cut_ga threshold, using an example that |
408 |
+--- a/testsuite/i20-fmindex-core.pl |
409 |
++++ b/testsuite/i20-fmindex-core.pl |
410 |
+@@ -1,4 +1,4 @@ |
411 |
+-#! /usr/bin/perl |
412 |
++#!/usr/bin/env perl |
413 |
+ |
414 |
+ # Test of makenhmmerdb and the core fm-index search functionality, using extactmatch |
415 |
+ # |
416 |
+--- a/testsuite/i5-hmmbuild-naming.pl |
417 |
++++ b/testsuite/i5-hmmbuild-naming.pl |
418 |
+@@ -1,4 +1,4 @@ |
419 |
+-#! /usr/bin/perl |
420 |
++#!/usr/bin/env perl |
421 |
+ |
422 |
+ # Test that HMM naming in hmmbuild works as advertised. |
423 |
+ # Written to test for #h50. |
424 |
+--- a/testsuite/i6-hmmalign-mapali.pl |
425 |
++++ b/testsuite/i6-hmmalign-mapali.pl |
426 |
+@@ -1,4 +1,4 @@ |
427 |
+-#! /usr/bin/perl |
428 |
++#!/usr/bin/env perl |
429 |
+ |
430 |
+ # Test the hmmalign --mapali option. |
431 |
+ # |
432 |
+--- a/testsuite/i7-hmmbuild-fragments.pl |
433 |
++++ b/testsuite/i7-hmmbuild-fragments.pl |
434 |
+@@ -1,4 +1,4 @@ |
435 |
+-#! /usr/bin/perl |
436 |
++#!/usr/bin/env perl |
437 |
+ |
438 |
+ # Test the ability of hmmbuild to deal with crappy alignments |
439 |
+ # of lots of sequence fragments. |
440 |
+--- a/testsuite/i8-nonresidues.pl |
441 |
++++ b/testsuite/i8-nonresidues.pl |
442 |
+@@ -1,4 +1,4 @@ |
443 |
+-#! /usr/bin/perl |
444 |
++#!/usr/bin/env perl |
445 |
+ |
446 |
+ # Regression test of handling a nonresidue '*' character. By design, |
447 |
+ # '*' residues score 0 in insert states and N,C,J; and -inf in match |
448 |
+--- a/testsuite/i9-optional-annotation.pl |
449 |
++++ b/testsuite/i9-optional-annotation.pl |
450 |
+@@ -1,4 +1,4 @@ |
451 |
+-#! /usr/bin/perl |
452 |
++#!/usr/bin/env perl |
453 |
+ |
454 |
+ # Check that we can deal with HMMs with no optional annotation, in either |
455 |
+ # hmmscan or hmmsearch mode. |
456 |
+--- a/testsuite/test-make.pl |
457 |
++++ b/testsuite/test-make.pl |
458 |
+@@ -1,4 +1,4 @@ |
459 |
+-#! /usr/bin/perl -w |
460 |
++#!/usr/bin/env perl |
461 |
+ |
462 |
+ # Usage: test-make.pl <builddir> <srcdir> <tmppfx> |
463 |
+ # |
464 |
|
465 |
diff --git a/sci-biology/hmmer/hmmer-3.1_beta2.ebuild b/sci-biology/hmmer/hmmer-3.1_beta2.ebuild |
466 |
new file mode 100644 |
467 |
index 00000000..d893cb3 |
468 |
--- /dev/null |
469 |
+++ b/sci-biology/hmmer/hmmer-3.1_beta2.ebuild |
470 |
@@ -0,0 +1,49 @@ |
471 |
+# Copyright 1999-2016 Gentoo Foundation |
472 |
+# Distributed under the terms of the GNU General Public License v2 |
473 |
+# $Id$ |
474 |
+ |
475 |
+EAPI=6 |
476 |
+ |
477 |
+MY_PV="${PV/_beta/b}" |
478 |
+ |
479 |
+DESCRIPTION="Sequence analysis using profile hidden Markov models" |
480 |
+HOMEPAGE="http://hmmer.org/" |
481 |
+SRC_URI="http://eddylab.org/software/${PN}3/${MY_PV}/hmmer-${MY_PV}.tar.gz" |
482 |
+ |
483 |
+LICENSE="GPL-3" |
484 |
+SLOT="0" |
485 |
+IUSE="altivec cpu_flags_x86_sse gsl mpi test +threads" |
486 |
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" |
487 |
+ |
488 |
+RDEPEND=" |
489 |
+ mpi? ( virtual/mpi ) |
490 |
+ gsl? ( sci-libs/gsl:= )" |
491 |
+DEPEND="${RDEPEND} |
492 |
+ test? ( dev-lang/perl )" |
493 |
+ |
494 |
+S="${WORKDIR}/${PN}-${MY_PV}" |
495 |
+PATCHES=( |
496 |
+ "${FILESDIR}/${PN}-3.1_beta2-fix-perl-shebangs.patch" |
497 |
+ "${FILESDIR}/${PN}-3.1_beta2-fix-header-install-path.patch" |
498 |
+) |
499 |
+ |
500 |
+src_configure() { |
501 |
+ # make build verbose, bug 429308 |
502 |
+ export V=1 |
503 |
+ |
504 |
+ econf \ |
505 |
+ --disable-pic \ |
506 |
+ $(use_enable altivec vmx) \ |
507 |
+ $(use_enable cpu_flags_x86_sse sse) \ |
508 |
+ $(use_enable mpi) \ |
509 |
+ $(use_enable threads) \ |
510 |
+ $(use_with gsl) |
511 |
+} |
512 |
+ |
513 |
+src_install() { |
514 |
+ default |
515 |
+ dodoc Userguide.pdf |
516 |
+ |
517 |
+ insinto /usr/share/${PN} |
518 |
+ doins -r tutorial |
519 |
+} |