sci-biology/tgi-tools: New ebuild, see http://bugs.gentoo.org/show_bug.cgi?id=157827

svn path=/sunrise/; revision=2279

5 files changed, 116 insertions, 0 deletions

diff --git a/sci-biology/tgi-tools/ChangeLog b/sci-biology/tgi-tools/ChangeLog
new file mode 100644
index 000000000..939a1ea92
--- /dev/null
+++ b/sci-biology/tgi-tools/ChangeLog
@@ -0,0 +1,8 @@
+# ChangeLog for sci-biology/tgi-tools
+# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  12 Dec 2006; Andrei K. (azazello) <gentoo@horizon.ath.cx>
+  +tgi-tools-0.1.ebuild, +metadata.xml:
+  New ebuild, see http://bugs.gentoo.org/show_bug.cgi?id=157827
+
diff --git a/sci-biology/tgi-tools/Manifest b/sci-biology/tgi-tools/Manifest
new file mode 100644
index 000000000..35b85b030
--- /dev/null
+++ b/sci-biology/tgi-tools/Manifest
@@ -0,0 +1,26 @@
+DIST cdbfasta.tar.gz 23470 RMD160 d587deaac94eced97728b0596022ea5e6a1bc75e SHA1 c7455ad2ac92cd1ee1293f0100fd871d71e4d630 SHA256 6862061d923f49579568e62be06bf434e79dbb56dfafe573353b4eb7d8ab9c9c
+DIST mdust.tar.gz 7526 RMD160 c04a6ba5a56724bfee70b8fe31f0bf4132b74885 SHA1 8885f206d61a76c6623c4115af02793bb52911c4 SHA256 9722806920fc6772dc92f99e7a59554c5f7c35b596dca0df9ed03ff2e5c6440d
+DIST nrcl.tar.gz 13151 RMD160 65f2e829fcf2da0134873eaa13098995b4472e15 SHA1 a9bf20a6f0f10201a03fb51644fa64e2519abd84 SHA256 3402a3efb38e3c7320831ca07e228374bbbba34d5b8a161446a7fc0bf4397808
+DIST psx.tar.gz 7797 RMD160 2b6de75126f19cbb60e1ed0b9988a935ad021a45 SHA1 3e0ac61f9ef2e546ff571bfc269e904138b445b9 SHA256 6759f1001be93fcfca9cebd0c764088c4942f2d7feee100d10cf2fbb39e4cd5a
+DIST pvmsx.tar.gz 10963 RMD160 1d14cb6e25a533f8a9879b04c5eb9e04532874e5 SHA1 562ea8628e47739ec7b98c622c894fe45e210c98 SHA256 c403534a0d13c2457a50c8ff5e9aeb5979d91a56307478b6420b5caf40e62230
+DIST sclust.tar.gz 14370 RMD160 1334a6a555c6ed3c8ad03ed697887bba76e8441e SHA1 19afe2272cb8b01e631313d57c38cd7fc575fc3c SHA256 4550350993a56d4e5e7163247965d4af91c32cc40ff7e0eeff3a0c6e04fd8ef4
+DIST seqclean.tar.gz 181383 RMD160 d3faae9e342e95dcbd66d39d80eb7e53f0527275 SHA1 8b3871cc0d70d71ff1bc7bfedc3638ff60e4c889 SHA256 4175b6ca7d93a7ea39e6dfb513500205c29a61b393a96bb2a7861a5540fd0d6d
+DIST tclust.tar.gz 8864 RMD160 e77a8ce86fa779bbce7c46efbce2245ec7735681 SHA1 35793ddc161c31ce0827073e993f4f6456dbbd35 SHA256 d4f9714f56f77c0e31f0ec9cd9da374899184f40fd688b06292e40412fbb7445
+DIST tgi_cpp_library.tar.gz 58212 RMD160 a85d0e0232a3956f93e521a73075d81d5ecfaaf3 SHA1 1039291f5f0ca617d025bcfacf4f271a3a225001 SHA256 555a81a63233d725868f6179cf3f5d74cceaa040058e2e4ded20f95487c89875
+DIST trimpoly.tar.gz 12562 RMD160 7345812dbbcea3d7fd2018ba1b04254863d171a4 SHA1 3558e9663cba6e6c179ca6f9a019f95d7aa1d4db SHA256 aa8f4a47d45ee534a15edf8e325f341a72d0ce0fa659ccfd8591c15bef44da4f
+DIST zmsort.tar.gz 5537 RMD160 cf6599dbd417f5ea50ec41db7909a2415ac28e68 SHA1 27a88033d99da8671fcae598f21e5b8cb7089e40 SHA256 32c5b72e22ae0fbd1784174dcff74e1a40817e29e98b2a0a32a21d83ace6b7fd
+EBUILD tgi-tools-0.1.ebuild 1431 RMD160 c8726e6dc89254252c9e63af2a944bec51828b28 SHA1 aca3ec617c21b1e127cdf6cf903d09d85e6d00f6 SHA256 942c95b0ec7ed03d4099ccdcd6942e5729323a2ee8f334f6cc752a52999056d6
+MD5 90bf9ef5f63bbcf79be97689d2b0a516 tgi-tools-0.1.ebuild 1431
+RMD160 c8726e6dc89254252c9e63af2a944bec51828b28 tgi-tools-0.1.ebuild 1431
+SHA256 942c95b0ec7ed03d4099ccdcd6942e5729323a2ee8f334f6cc752a52999056d6 tgi-tools-0.1.ebuild 1431
+MISC ChangeLog 287 RMD160 5d4be70c6f1eb443b45881c67491691293754ff4 SHA1 45407e28c9d0f316a1b0664567fda6865a72de2a SHA256 a869b9d68a11d2958438028c05042bfc3409c1bd82b945d9ac9431eee22bfd69
+MD5 33b104f9a53887bb6d404ae7f4bff882 ChangeLog 287
+RMD160 5d4be70c6f1eb443b45881c67491691293754ff4 ChangeLog 287
+SHA256 a869b9d68a11d2958438028c05042bfc3409c1bd82b945d9ac9431eee22bfd69 ChangeLog 287
+MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42
+MD5 1e678929a9fec6632e227bdf2262e9a1 metadata.xml 170
+RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 metadata.xml 170
+SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 metadata.xml 170
+MD5 b74c49cd884b0fc9e4063bbf4f668097 files/digest-tgi-tools-0.1 2402
+RMD160 64d7dc05d77a3600c7db302a0b2fc562ff01c6b6 files/digest-tgi-tools-0.1 2402
+SHA256 228c18a3a616b8bb8c1c977bfe05a5908bc5795380e9886dd7e3d8ed02c5042d files/digest-tgi-tools-0.1 2402
diff --git a/sci-biology/tgi-tools/files/digest-tgi-tools-0.1 b/sci-biology/tgi-tools/files/digest-tgi-tools-0.1
new file mode 100644
index 000000000..366567bf2
--- /dev/null
+++ b/sci-biology/tgi-tools/files/digest-tgi-tools-0.1
@@ -0,0 +1,33 @@
+MD5 e42d20b19adeafdf4162f32482bce1b0 cdbfasta.tar.gz 23470
+RMD160 d587deaac94eced97728b0596022ea5e6a1bc75e cdbfasta.tar.gz 23470
+SHA256 6862061d923f49579568e62be06bf434e79dbb56dfafe573353b4eb7d8ab9c9c cdbfasta.tar.gz 23470
+MD5 9cd31b3a1647c3e0f955694a57903c0a mdust.tar.gz 7526
+RMD160 c04a6ba5a56724bfee70b8fe31f0bf4132b74885 mdust.tar.gz 7526
+SHA256 9722806920fc6772dc92f99e7a59554c5f7c35b596dca0df9ed03ff2e5c6440d mdust.tar.gz 7526
+MD5 1888e9dc225052b3b9bda1ca9e6b0e03 nrcl.tar.gz 13151
+RMD160 65f2e829fcf2da0134873eaa13098995b4472e15 nrcl.tar.gz 13151
+SHA256 3402a3efb38e3c7320831ca07e228374bbbba34d5b8a161446a7fc0bf4397808 nrcl.tar.gz 13151
+MD5 09e181d2c5e71460164e301a24a055cf psx.tar.gz 7797
+RMD160 2b6de75126f19cbb60e1ed0b9988a935ad021a45 psx.tar.gz 7797
+SHA256 6759f1001be93fcfca9cebd0c764088c4942f2d7feee100d10cf2fbb39e4cd5a psx.tar.gz 7797
+MD5 7350f170008b232c1935de743cc40c4e pvmsx.tar.gz 10963
+RMD160 1d14cb6e25a533f8a9879b04c5eb9e04532874e5 pvmsx.tar.gz 10963
+SHA256 c403534a0d13c2457a50c8ff5e9aeb5979d91a56307478b6420b5caf40e62230 pvmsx.tar.gz 10963
+MD5 a8bc3fb633bf1a3dcd56cbde29352dac sclust.tar.gz 14370
+RMD160 1334a6a555c6ed3c8ad03ed697887bba76e8441e sclust.tar.gz 14370
+SHA256 4550350993a56d4e5e7163247965d4af91c32cc40ff7e0eeff3a0c6e04fd8ef4 sclust.tar.gz 14370
+MD5 ce4a5cc23c6458dd959e0e5dd0cd22ce seqclean.tar.gz 181383
+RMD160 d3faae9e342e95dcbd66d39d80eb7e53f0527275 seqclean.tar.gz 181383
+SHA256 4175b6ca7d93a7ea39e6dfb513500205c29a61b393a96bb2a7861a5540fd0d6d seqclean.tar.gz 181383
+MD5 a0893732e9e427978bf6d460727619a5 tclust.tar.gz 8864
+RMD160 e77a8ce86fa779bbce7c46efbce2245ec7735681 tclust.tar.gz 8864
+SHA256 d4f9714f56f77c0e31f0ec9cd9da374899184f40fd688b06292e40412fbb7445 tclust.tar.gz 8864
+MD5 c568ef74bab896d09c2773b0764d8b31 tgi_cpp_library.tar.gz 58212
+RMD160 a85d0e0232a3956f93e521a73075d81d5ecfaaf3 tgi_cpp_library.tar.gz 58212
+SHA256 555a81a63233d725868f6179cf3f5d74cceaa040058e2e4ded20f95487c89875 tgi_cpp_library.tar.gz 58212
+MD5 dcaee491b6a6765673164acc1158fa3a trimpoly.tar.gz 12562
+RMD160 7345812dbbcea3d7fd2018ba1b04254863d171a4 trimpoly.tar.gz 12562
+SHA256 aa8f4a47d45ee534a15edf8e325f341a72d0ce0fa659ccfd8591c15bef44da4f trimpoly.tar.gz 12562
+MD5 94fd4565d949e140f237d3b2a4c16212 zmsort.tar.gz 5537
+RMD160 cf6599dbd417f5ea50ec41db7909a2415ac28e68 zmsort.tar.gz 5537
+SHA256 32c5b72e22ae0fbd1784174dcff74e1a40817e29e98b2a0a32a21d83ace6b7fd zmsort.tar.gz 5537
diff --git a/sci-biology/tgi-tools/metadata.xml b/sci-biology/tgi-tools/metadata.xml
new file mode 100644
index 000000000..7e3286984
--- /dev/null
+++ b/sci-biology/tgi-tools/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>maintainer-wanted</herd>
+</pkgmetadata>
diff --git a/sci-biology/tgi-tools/tgi-tools-0.1.ebuild b/sci-biology/tgi-tools/tgi-tools-0.1.ebuild
new file mode 100644
index 000000000..0471acb20
--- /dev/null
+++ b/sci-biology/tgi-tools/tgi-tools-0.1.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+# http://bugs.gentoo.org/show_bug.cgi?id=157827
+
+DESCRIPTION="The Gene Index Project utilities for genomic data processing: seqclean, cdbfasta, psx"
+LICENSE="Artistic"
+HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"
+SLOT="0"
+IUSE=""
+KEYWORDS="~x86"
+
+for i in seqclean/{seqclean,mdust,trimpoly} cdbfasta/cdbfasta tgicl/{psx,pvmsx,zmsort,tclust,sclust,nrcl,tgi_cpp_library}; do
+	SRC_URI="${SRC_URI} ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/${i}.tar.gz";
+done
+
+RESTRICT="nomirror"
+
+DEPEND=""
+RDEPEND=${DEPEND}
+S=${WORKDIR}
+
+src_unpack() {
+	unpack {seqclean,mdust,trimpoly,cdbfasta,tgi_cpp_library}.tar.gz
+	for i in nrcl sclust tclust zmsort psx pvmsx; do
+		mkdir ${S}/${i}; cd ${S}/${i}; unpack ${i}.tar.gz
+	done
+}
+
+src_compile() {
+	sed -i 's/use Mailer;/#use Mailer;/' ${S}/seqclean/seqclean
+	sed -i 's/-V\t\tverbose/-V\t\tverbose\\/' ${S}/zmsort/zmsort.cpp
+	# TODO: fix errors in nrcl, pvmsx
+	for i in cdbfasta mdust psx sclust tclust trimpoly zmsort; do
+		sed -i 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' ${S}/${i}/Makefile
+		(cd ${S}/${i}; emake) || die
+	done
+}
+
+src_install() {
+	dobin cdbfasta/{cdbfasta,cdbyank} seqclean/{seqclean,cln2qual,bin/seqclean.psx}
+	for i in mdust psx sclust tclust trimpoly zmsort; do dobin ${i}/${i}; done
+}