diff options
| -rw-r--r-- | sci-biology/meme/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/meme/files/meme-4.8.1-Makefile.am.patch | 134 | ||||
| -rw-r--r-- | sci-biology/meme/meme-4.8.1-r2.ebuild | 85 |
3 files changed, 0 insertions, 220 deletions
diff --git a/sci-biology/meme/Manifest b/sci-biology/meme/Manifest index 4496d777cb23..54d47df7b6ea 100644 --- a/sci-biology/meme/Manifest +++ b/sci-biology/meme/Manifest @@ -1,2 +1 @@ DIST meme_4.11.2.tar.gz 18004930 SHA256 6e3ff843366588ea13fa8060306be9e2c144521912dfb268f03638003bcdd581 SHA512 c97c3815e71e2fb5491548152f00688cdfbf4365f6027657e0ffc68e5d96cdd10a4708e0882ab7a5a61d78d93113c925cf5bb300fbe93fa4b2961becef497894 WHIRLPOOL 6b77d7832342658d5cf546af0b005b59664c811d25a0412df765a15a8c80a75d9618a1f9966c9a2824750eced6605b534d41199382a6f2641e7430540ba19fcf -DIST meme_4.8.1.tar.gz 8703632 SHA256 c3ad3ca26bc2a7130c5eceb64e1745275c317a5469e98fc8759a9e56babccb8c SHA512 31833169ffa9bd82387d1872be40b0fc4312f4a05bb7abb84daf372244ce3f2a68c89c96722c0453f7bcd9eb4fc84fd3d66e1278af55d556715b94b0df5f87ba WHIRLPOOL 4b5e8968e6964479081d1fe036ff3aa7a50dc56bafc0031890d2e47dbdc8e0273e62ffe01800d8908b2fa9824a4766254bb0fd94003d9ca14784073d5357793e diff --git a/sci-biology/meme/files/meme-4.8.1-Makefile.am.patch b/sci-biology/meme/files/meme-4.8.1-Makefile.am.patch deleted file mode 100644 index e84006295735..000000000000 --- a/sci-biology/meme/files/meme-4.8.1-Makefile.am.patch +++ /dev/null @@ -1,134 +0,0 @@ - Makefile.am | 6 +++--- - doc/Makefile.am | 2 +- - doc/examples/Makefile.am | 24 +++++++++++----------- - .../Makefile.am | 2 +- - doc/examples/sample_opal_scripts/Makefile.am | 2 +- - doc/images/Makefile.am | 2 +- - scripts/Makefile.am | 2 +- - 7 files changed, 20 insertions(+), 20 deletions(-) - -diff --git a/Makefile.am b/Makefile.am -index 4a69e34..842e33f 100644 ---- a/Makefile.am -+++ b/Makefile.am -@@ -18,11 +18,11 @@ ARCHIVE_REVISION: - install-data-hook: dbdir - - dbdir: -- mkdir -p $(MEME_DB) -+ mkdir -p $(DESTDIR)$(MEME_DB) - - install-data-local: -- mkdir -p $(MEME_LOGS) -- chmod a+w $(MEME_LOGS) -+ mkdir -p $(DESTDIR)$(MEME_LOGS) -+ chmod a+w $(DESTDIR)$(MEME_LOGS) - - distdir = $(PACKAGE)_$(VERSION) - -diff --git a/doc/Makefile.am b/doc/Makefile.am -index e0d6af9..e7bcb4f 100644 ---- a/doc/Makefile.am -+++ b/doc/Makefile.am -@@ -202,7 +202,7 @@ COMMON_DOC = \ - if WEBSITE - MEME_DOC_DIR = $(WEBDIR)/doc - else --MEME_DOC_DIR = $(prefix)/doc -+MEME_DOC_DIR = $(docdir)/html - endif - - memedocdir = $(MEME_DOC_DIR) -diff --git a/doc/examples/Makefile.am b/doc/examples/Makefile.am -index 12970b5..633492c 100644 ---- a/doc/examples/Makefile.am -+++ b/doc/examples/Makefile.am -@@ -51,24 +51,24 @@ if WEBSITE - exdir = $(WEBDIR)/examples - other_exdir = $(WEBDIR)/doc/examples - else --exdir = $(prefix)/doc/examples -+exdir = $(prefix)/share/meme/examples - other_exdir = $(exdir) - endif - - ex_DATA = $(EXAMPLES) - - install-data-hook: -- tar xzvf centrimo_example_output_files.tgz -C $(other_exdir) -- tar xzvf dreme_example_output_files.tgz -C $(other_exdir) -- tar xzvf fimo_example_output_files.tgz -C $(other_exdir) -- tar xzvf glam2_example_output_files.tgz -C $(other_exdir) -- tar xzvf glam2scan_example_output_files.tgz -C $(other_exdir) -- tar xzvf mast_example_output_files.tgz -C $(other_exdir) -- tar xzvf mcast_example_output_files.tgz -C $(other_exdir) -- tar xzvf meme_example_output_files.tgz -C $(other_exdir) -- tar xzvf memechip_example_output_files.tgz -C $(other_exdir) -- tar xzvf spamo_example_output_files.tgz -C $(other_exdir) -- tar xzvf tomtom_example_output_files.tgz -C $(other_exdir) -+ tar xzvf centrimo_example_output_files.tgz -C $(DESTDIR)/$(other_exdir) -+ tar xzvf dreme_example_output_files.tgz -C $(DESTDIR)/$(other_exdir) -+ tar xzvf fimo_example_output_files.tgz -C $(DESTDIR)/$(other_exdir) -+ tar xzvf glam2_example_output_files.tgz -C $(DESTDIR)/$(other_exdir) -+ tar xzvf glam2scan_example_output_files.tgz -C $(DESTDIR)/$(other_exdir) -+ tar xzvf mast_example_output_files.tgz -C $(DESTDIR)/$(other_exdir) -+ tar xzvf mcast_example_output_files.tgz -C $(DESTDIR)/$(other_exdir) -+ tar xzvf meme_example_output_files.tgz -C $(DESTDIR)/$(other_exdir) -+ tar xzvf memechip_example_output_files.tgz -C $(DESTDIR)/$(other_exdir) -+ tar xzvf spamo_example_output_files.tgz -C $(DESTDIR)/$(other_exdir) -+ tar xzvf tomtom_example_output_files.tgz -C $(DESTDIR)/$(other_exdir) - - # If .svnignore file doesn't exist - # create an empty one -diff --git a/doc/examples/compute_prior_dist_example_output_files/Makefile.am b/doc/examples/compute_prior_dist_example_output_files/Makefile.am -index 747028d..a358f58 100644 ---- a/doc/examples/compute_prior_dist_example_output_files/Makefile.am -+++ b/doc/examples/compute_prior_dist_example_output_files/Makefile.am -@@ -22,7 +22,7 @@ EXAMPLES = \ - if WEBSITE - exdir = $(WEBDIR)/doc/examples/compute_prior_dist_example_output_files - else --exdir = $(prefix)/doc/examples/compute_prior_dist_example_output_files -+exdir = $(prefix)/share/meme/examples/compute_prior_dist_example_output_files - endif - - ex_DATA = $(EXAMPLES) -diff --git a/doc/examples/sample_opal_scripts/Makefile.am b/doc/examples/sample_opal_scripts/Makefile.am -index 3a638b3..30925bb 100644 ---- a/doc/examples/sample_opal_scripts/Makefile.am -+++ b/doc/examples/sample_opal_scripts/Makefile.am -@@ -18,7 +18,7 @@ EXAMPLES = \ - if WEBSITE - exdir = $(WEBDIR)/doc/examples/sample_opal_scripts - else --exdir = $(prefix)/doc/examples/sample_opal_scripts -+exdir = $(prefix)/share/meme/examples/sample_opal_scripts - endif - - ex_DATA = $(EXAMPLES) -diff --git a/doc/images/Makefile.am b/doc/images/Makefile.am -index c879621..a4696cd 100644 ---- a/doc/images/Makefile.am -+++ b/doc/images/Makefile.am -@@ -28,7 +28,7 @@ MEME_IMAGES = \ - if WEBSITE - memeimgdir = $(WEBDIR)/doc/images - else --memeimgdir = $(prefix)/doc/images -+memeimgdir = $(docdir)/html/images - endif - - memeimg_DATA = $(MEME_IMAGES) -diff --git a/scripts/Makefile.am b/scripts/Makefile.am -index 4143e46..8a5c021 100644 ---- a/scripts/Makefile.am -+++ b/scripts/Makefile.am -@@ -8,7 +8,7 @@ - if WEBSITE - MEME_DOC_DIR = $(WEBDIR)/doc - else --MEME_DOC_DIR = $(prefix)/doc -+MEME_DOC_DIR = $(docdir) - endif - - ARCHIVE_REVISION = $(shell cat ../ARCHIVE_REVISION) diff --git a/sci-biology/meme/meme-4.8.1-r2.ebuild b/sci-biology/meme/meme-4.8.1-r2.ebuild deleted file mode 100644 index 8a1482c0b32d..000000000000 --- a/sci-biology/meme/meme-4.8.1-r2.ebuild +++ /dev/null @@ -1,85 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=4 - -PYTHON_DEPEND="2" - -inherit autotools eutils python - -DESCRIPTION="The MEME/MAST system - Motif discovery and search" -HOMEPAGE="http://meme.sdsc.edu/meme" -SRC_URI="http://meme.nbcr.net/downloads/${PN}_${PV}.tar.gz" - -LICENSE="meme" -SLOT="0" -KEYWORDS="amd64 x86" -IUSE="debug examples mpi" - -DEPEND=" - app-shells/tcsh - dev-libs/libxml2:2 - dev-libs/libxslt - mpi? ( virtual/mpi )" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${PN}_${PV}" - -#pkg_setup() { - # generate meme group to restrict logging to /var/log/meme -# enewgroup meme -# python_pkg_setup -# python_set_active_version 2 -#} - -src_prepare() { - use examples || sed -e '/SUBDIRS/s:examples::g' -i doc/Makefile.am - sed \ - -e '/flags/s:-O3::g' \ - -e '/opt/s:-O::g' \ - -e '/debug/s:-ggdb::' \ - -e '/debug/s:-g::' \ - -e 's:CFLAGS=:CFLAGS+=:g' \ - -i configure.ac || die - epatch \ - "${FILESDIR}"/${P}-Makefile.am.patch - eautoreconf -} - -src_configure() { - MY_PREFIX="${ROOT}opt/meme" - USE_DISABLE_MPI=""; if ! use mpi; then USE_DISABLE_MPI="--enable-serial"; fi - econf \ - --sysconfdir="${EPREFIX}/etc/meme" \ - --with-logs="${ROOT}var/log/meme" \ - $(use_enable debug) \ - $USE_DISABLE_MPI -} - -src_test() { - # bug #297070 - emake -j1 test -} - -src_install() { - local i - default - - for i in "${ED}"/usr/bin/*; do - mv "${ED}"/usr/bin/{,meme-}$(basename ${i}) || die - done - - echo "PATH=/opt/${PN}/bin" > 99${PN} - doenvd 99${PN} - - # allow logging only for members of meme group - # diropts -m 0770 -g meme -o root - diropts -m ugo+rwxt -o root - keepdir /var/log/meme -} - -#pkg_postinst() { -# einfo 'Log files are produced in the "/var/log/meme" directory. Users' -# einfo 'need to be part of the meme group to use this facility.' -#} |