Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci

11 files changed, 319 insertions, 201 deletions

diff --git a/eclass/mpi.eclass b/eclass/mpi.eclass
index 29d8629b1..cc5d39e1e 100644
--- a/eclass/mpi.eclass
+++ b/eclass/mpi.eclass
@@ -92,7 +92,7 @@ mpi_econf_args() {
 # @CODE
 
 _mpi_do() {
-	local rc prefix
+	local rc prefix d
 	local cmd=${1}
 	local ran=1
 	local slash=/
diff --git a/licenses/signalp b/licenses/signalp
new file mode 100755
index 000000000..7e5b15f19
--- /dev/null
+++ b/licenses/signalp
@@ -0,0 +1,218 @@
+  ACADEMIC SOFTWARE LICENSE AGREEMENT FOR END-USERS AT PUBLICLY FUNDED
+  ACADEMIC, EDUCATION OR RESEARCH INSTITUTIONS FOR THE USE OF SignalP 3.0
+  
+  By downloading the Software you are consenting to be bound by and become
+  a party to this agreement as the "Licensee". If you do not agree to all
+  of the terms of this agreement, you must not click the Acceptance
+  button, not install the product nor use the product, and you do not
+  become a LICENSEE under this agreement. 
+  
+  If you are not a member of a publicly funded Academic and/or Education
+  and/or Research Institution you must obtain a commercial license, please
+  send mail to (software@cbs.dtu.dk). This software license agreement is
+  entered into by and between Center for Biological Sequence Analysis,
+  Technical University of Denmark (hereinafter "CBS") and the "LICENSEE". 
+  
+  WHEREAS CBS has the right to license all copyrights and other property
+  rights in the Licensed Software identified as SignalP 3.0 and developed
+  by CBS and CBS desires to license the Software so that it becomes
+  available for public use and benefit. 
+  
+  WHEREAS LICENSEE is a public funded Academic and/or Education and/or
+  Research Institution. 
+  
+  WHEREAS LICENSEE desires to acquire a free non-exclusive license to use
+  the Software for internal research purposes only. 
+  
+  NOW, THEREFORE, in consideration of the mutual promises and covenants
+  contained herein, the parties agree as follows: 
+  
+  1. Definitions 
+  
+  "Licensed Software" means the specific version SignalP 3.0 pursuant
+  to this Agreement. Any opinion, findings, conclusions or recommendations
+  expressed in the Licensed Software are those of the authors and do not
+  necessarily reflect the views of CBS. 
+  
+  2. License 
+  
+  Subject to the terms and conditions of this Agreement a non-exclusive,
+  non-transferable License to use and copy the Licensed Software is made
+  available free of charge for the LICENSEE which is a non-profit
+  educational, academic and/or research institution. The License is only
+  granted for personal and internal use in research only at one Site,
+  where a Site is defined as a set of contiguous buildings in one
+  location. The software will be used at only one location of LICENSEE. 
+  
+  This license does not entitle Licensee to receive from CBS copies of the
+  Licensed software on disks, tapes or CD's, hard-copy documentation,
+  technical support, telephone assistance, or enhancements or updates to
+  the Licensed Software. 
+  
+  The user and any research assistants, co-workers or other workers who
+  may use the Software agree to not give the program to third parties or
+  grant licenses on software, which include the Software, alone or
+  integrated into other software, to third parties. Modification of the
+  source code is prohibited without the prior written consent of CBS. 
+  
+  3. Ownership 
+  
+  Except as expressly licensed in this Agreement, CBS shall retain title
+  to the Licensed Software, and any upgrades and modifications created by
+  CBS. 
+  
+  4. Consideration 
+  
+  In consideration for the license rights granted by CBS, LICENSEE will
+  obtain this academic license free of charge. 
+  
+  5. Copies 
+  
+  LICENSEE shall have the right to make copies of the Licensed Software
+  for internal use at the Site and for back-up purposes under this
+  Agreement, but agrees that all such copies shall contain the copyright
+  notices and all other reasonable and appropriate proprietary markings or
+  confidential legends that appear on the Licensed Software provided
+  hereunder. 
+  
+  6. Support 
+  
+  CBS shall have no obligation to offer support services to LICENSEE, and
+  nothing contained herein shall be interpreted as to require CBS to
+  provide maintenance, installation services, version updates, debugging,
+  consultation or end-user support of any kind. 
+  
+  7. Software Protection 
+  
+  LICENSEE acknowledges that the Licensed Software is proprietary to CBS.
+  The software code shall be treated as trade secrets and confidential
+  information of CBS, and LICENSEE agrees to use best efforts to hold the
+  same in confidence. LICENSEE's obligation for confidentiality shall not
+  extend to any information which is or becomes generally available to the
+  public, is already known to or subsequently disclosed by third parties
+  to LICENSEE and at its free disposal, or is independently developed by
+  LICENSEE or its affiliates without the use of the confidential
+  information disclosed by CBS, or is required by law or legal process. 
+  
+  Except as other wise expressly permitted in this Agreement, Licensee my
+  not (i) modify or create any derivative works of the Licensed Software
+  or documentation, including customization, translation or localization;
+  (ii) decompile, disassemble, reverse engineer, or otherwise attempt to
+  derive the source code for the Product; (iii) redistribute, encumber,
+  sell, rent, lease, sublicense, or otherwise transfer rights to the
+  Licensed Software; (iv) remove or alter any trademark, logo, copyright
+  or other proprietary notices, legends, symbols or labels in the Product;
+  or (v) publish any results of benchmark tests run on the Product to a
+  third party without CBS's prior written consent. 
+  
+  8. Representations of CBS to LICENSEE 
+  
+  CBS represents to LICENSEE that (i) CBS has the right to grant the
+  License and to enter into this agreement, (ii) that, to the best of
+  CBS's knowledge, the Licensed software does not infringe any patent,
+  copyright or trade secrets of any third party, provided however that
+  such representation and warranty shall not apply to any addition to, or
+  modifications or adaptation of, the Licensed Software made by LICENSEE
+  and (iii) CBS undertakes to use best efforts to cooperate with and
+  assist LICENSEE, at LICENSEE's expense, in defending itself against any
+  action based on the alleged infringement of any third party patent,
+  copyright or trade secret rights resulting from or relating to the use
+  or licensing of the Licensed Software by LICENSEE. 
+  
+  9. Indemnity and Disclaimer of Warranties 
+  
+  Except as expressly set forth in this agreement, CBS makes no
+  representations or warranties, express or implied. 
+  
+  The product is provided free of charge, and, therefore, on an "as is"
+  basis, without warranty of any kind, express or implied, including
+  without limitation the warranties that it is free of defects, virus
+  free, able to operate on an uninterrupted basis, merchantable, fit for a
+  particular purpose or non-interfering. The entire risk as to the quality
+  and performance of the Licensed Software is borne by LICENSEE. 
+  
+  By way of example, but not limitation, CBS makes no representations or
+  warranties of merchantability or fitness for any particular application
+  or, except as set forth in paragraph 8, that the use of the Software
+  will not infringe any patents, copyrights or trademarks or other rights
+  of third parties. The entire risk as to the quality and performance of
+  the product is borne by LICENSEE. CBS shall not be liable for any
+  liability or damages with respect to any claim by LICENSEE or any third
+  party on account of, or arising from the license or use of the Software.
+  
+  Should the Licensed Software prove defective in any respect, LICENSEE
+  and not LICENSOR or it's affiliates should assume the entire cost of any
+  service and repair. This disclaimer of warranty constitutes an essential
+  part of this agreement. No use of the licensed product is authorized
+  hereunder except under this disclaimer. 
+  
+  In no event will LICENSOR or its affiliates be liable for any indirect,
+  special, incidental or consequential damages arising out of the use of
+  or inability to use the product, including, without limitation, damages
+  for lost profits, loss of goodwill, work stoppage, computer failure or
+  malfunction, or any and all other commercial damages or losses, even if
+  advised of the possibility thereof, and regardless of the legal or
+  equitable theory (contract, tort or otherwise) upon which the claim is
+  based. 
+  
+  10. Promotional Advertising & References 
+  
+  LICENSEE may not use the name of the Licensed Software in its
+  promotional advertising, product literature, and other similar
+  promotional materials to be disseminated to the public or any portion
+  thereof. LICENSEE agrees not to identify CBS in any promotional
+  advertising or other promotional materials to be disseminated to the
+  public, or any portion thereof without CBS's prior written consent.
+  LICENSEE agrees that any reference to the software for crystallographic
+  computations will cite one or more publications as set forth in the
+  manual and in agreement with common scientific practice. CBS shall not
+  use LICENSEE's name in publicity or advertising involving this Agreement
+  or otherwise without LICENSEE's prior written consent which may be
+  withheld at LICENSEE's sole discretion. 
+  
+  11. Term 
+  
+  This Agreement and the license rights granted herein shall become
+  effective as of the date this Agreement is executed by both parties and
+  shall be perpetual unless terminated in accordance with this Section. 
+  
+  CBS may terminate this Agreement at any time. 
+  
+  Either party may terminate this Agreement at any time effective upon the
+  other party's breach of any agreement, covenant, or representation made
+  in this Agreement, such breach remaining uncorrected sixty (60) days
+  after written notice thereof. 
+  
+  LICENSEE shall have the right, at any time, to terminate this Agreement
+  without cause by written notice to CBS specifying the date of
+  termination. 
+  
+  Upon termination, LICENSEE shall destroy all full and partial copies of
+  the Licensed Software. 
+  
+  12. Governing Law 
+  
+  This Agreement shall be construed in accordance with the laws of
+  Denmark. 
+  
+  13. General 
+  
+  The parties agree that this Agreement is the complete and exclusive
+  agreement among the parties and supersedes all proposals and prior
+  agreements whether written or oral, and all other communications among
+  the parties relating to the subject matter of this Agreement. This
+  Agreement cannot be modified except in writing and signed by both
+  parties. Failure by either party at any time to enforce any of the
+  provisions of this Agreement shall not constitute a waiver by such party
+  of such provision nor in any way affect the validity of this Agreement. 
+  
+  The invalidity of singular provisions does not affect the validity of
+  the entire understanding. The parties are obligated, however, to replace
+  the invalid provisions by a regulation which comes closest to the
+  economic intent of the invalid provision. The same shall apply mutatis
+  mutandis in case of a gap. 
+  
+  IN WITNESS WHEREOF, the LICENSEE hereto have caused this Agreement to be
+  duly executed on the date of the download of the software and by
+  accepting the license conditions by pressing the Acceptance button. 
+  
diff --git a/sci-biology/signalp/ChangeLog b/sci-biology/signalp/ChangeLog
new file mode 100644
index 000000000..723568360
--- /dev/null
+++ b/sci-biology/signalp/ChangeLog
@@ -0,0 +1,7 @@
+# ChangeLog for sci-biology/signalp
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  01 Apr 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog:
+  New package sci-biology/signalp, ebuild written by me
+
diff --git a/sci-biology/signalp/Manifest b/sci-biology/signalp/Manifest
new file mode 100644
index 000000000..e7654de92
--- /dev/null
+++ b/sci-biology/signalp/Manifest
@@ -0,0 +1,2 @@
+DIST signalp-3.0.Linux.tar.Z 1216617 RMD160 9b7ec647d015d5b0c30eef7034f3434befc88f10 SHA1 65e1a277ae03fb61b69bfef82782dd8e9f60fc93 SHA256 260c2e5bd945b386e833a7b7326cff6d7332302868e99c0aeae306212047c0c2
+EBUILD signalp-3.0.ebuild 1081 RMD160 8eb163d413b3a10fed3bd34cc7e624791ed27f7f SHA1 071eb95b793bd49e4aaacc87891175b9319c22f9 SHA256 4b5a6c0c8fe56144a1b42a3fe366c7504e205e1a3e590ef1d35d1d2bb5c90a36
diff --git a/sci-biology/signalp/metadata.xml b/sci-biology/signalp/metadata.xml
new file mode 100644
index 000000000..3302123e5
--- /dev/null
+++ b/sci-biology/signalp/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer>
+		<email>weaver@gentoo.org</email>
+		<name>Andrey Kislyuk</name>
+	</maintainer>
+	<herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/signalp/signalp-3.0.ebuild b/sci-biology/signalp/signalp-3.0.ebuild
new file mode 100644
index 000000000..7f84fb9a8
--- /dev/null
+++ b/sci-biology/signalp/signalp-3.0.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/amos/amos-2.0.8.ebuild,v 1.1 2008/08/26 16:33:07 weaver Exp $
+
+EAPI="2"
+
+DESCRIPTION="Prediction of signal peptide cleavage sites in amino acid sequences"
+HOMEPAGE="http://www.cbs.dtu.dk/services/SignalP/"
+SRC_URI="${P}.Linux.tar.Z"
+
+LICENSE="signalp"
+SLOT="0"
+IUSE="gnuplot"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="gnuplot? (
+	sci-visualization/gnuplot
+	media-libs/netpbm )"
+
+RESTRICT="fetch strip"
+
+pkg_nofetch() {
+	einfo "Please visit ${HOMEPAGE} and obtain the file"
+	einfo "\"${SRC_URI}\", then place it in ${DISTDIR}"
+}
+
+src_unpack() {
+	unpack ${A}
+	sed -i -e '/SIGNALP=/ s/\/usr//' \
+		-e '/TMPDIR=/ s/$SIGNALP//' "${S}/signalp" || die
+	sed -i 's/nawk/gawk/' "${S}"/bin/* || die
+}
+
+src_install() {
+	dobin signalp || die
+	insinto /opt/${P}
+	doins -r bin hmm how mod syn* test
+	exeinto /opt/${P}/bin
+	doexe bin/*
+	exeinto /opt/${P}/hmm
+	doexe hmm/*
+	exeinto /opt/${P}/how
+	doexe how/*
+	doman signalp.1
+	dodoc *readme
+}
diff --git a/sys-cluster/mpich2/ChangeLog b/sys-cluster/mpich2/ChangeLog
index ec738d22f..0ac102dd9 100644
--- a/sys-cluster/mpich2/ChangeLog
+++ b/sys-cluster/mpich2/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  01 Apr 2009; Justin Bronder <jsbronder@gentoo.org>
+  sys-cluster/mpich2/files/mpich2-1.0.8-mpdconf-env.patch,
+  -sys-cluster/mpich2/files/mpich2-1.0.8-site-packages-py.patch:
+  Fix #259805 by backing out the site-packages fix. It'll be better off just
+  sent directly to upstream.
+
   17 Feb 2009; Justin Bronder <jsbronder@gentoo.org>
   sys-cluster/mpich2/mpich2-1.0.8.ebuild:
   Missing line continuation, #259209.
diff --git a/sys-cluster/mpich2/Manifest b/sys-cluster/mpich2/Manifest
index 7dced8f01..90005b3b2 100644
--- a/sys-cluster/mpich2/Manifest
+++ b/sys-cluster/mpich2/Manifest
@@ -1,11 +1,10 @@
 AUX eselect.mpi.mpich2 226 RMD160 62e00e1f67ff5cc088d7aa3ef082241afef33bde SHA1 f89ddfb1a10251f5023093f6577ebb8265d55627 SHA256 ffad3f539f008c597077aee91a7c635968311c8b3124619acb727facd0d1e99e
 AUX mpd.conf 48 RMD160 289de9bb40759e3f71229cf47e4d2af83703a85f SHA1 244eee76dbf4ff269e4489d5cc7c3577c6c1fa6b SHA256 ae740cacaf2cb798921cb2092f5af98de67445e27af3f88858f3e6d2bbb127f4
 AUX mpich2-1.0.8-gforker-install-alt-fix.patch 621 RMD160 5b9904ae02f1c1098fdfd2dc4717610f89469afd SHA1 a33bcefa87d990a678436ebfac70976069a7f90d SHA256 a79e469b08e0a3f6c17ec7ec7ea01d3a56a553803fefd24f3794237eead36ced
-AUX mpich2-1.0.8-mpdconf-env.patch 5041 RMD160 c3d9f6ebd43443a24614da030253cf8c503afd59 SHA1 5b453a171f8b1dce93e3c2e675e5b3d4f05514e8 SHA256 b8c81614bba8c748db2ec24a7683d27b3a0430950fecd5644fd1f97f8e5ab2f9
+AUX mpich2-1.0.8-mpdconf-env.patch 5355 RMD160 26ffada537073676553fdc4a9ee6a02f1a1af279 SHA1 f40eee99425894d9c76c8eefa87b8e72d9b7a02a SHA256 14cbd73be6969569574a880ad23e7c71c4bb02e6994392b2661bf5fb1965ce3d
 AUX mpich2-1.0.8-pkgconfig.patch 928 RMD160 5ce7a800423f250dba0dd69560abebf845e7e556 SHA1 afba6883d1204a4b7c082af7e976186153263d64 SHA256 7f8dcafcb0d138130a684284d9bca86e4834f74a5132f0fef4556391abf43f8e
-AUX mpich2-1.0.8-site-packages-py.patch 7534 RMD160 93b2cab20620da379615eaf3bfc7279384987722 SHA1 706313c20e1d4d6a4a060c8ac36befdb5ee3b926 SHA256 a857e7c0effa7cdd62c1bc1bd054b4746764246410062d373e7e0892bcd20df8
 AUX mpich2.envd 45 RMD160 e29a0d617bbc15cc42d3088f8a79c1c715b353fa SHA1 765b885d0e1d65fe7ba845cf72e3e923613d6514 SHA256 d6f128f84e1d015922af42e1280586b84737740b2517cc0b35f498b571f252f9
 DIST mpich2-1.0.8.tar.gz 17237476 RMD160 646cf50fbdc60a49809f4d0a6bcaf2835844db1f SHA1 41d6f6ce1034ecec5c14fb03592730ae2dd071e5 SHA256 7551ce20f3ef366567c566d08782323360b5dbd2d15d816e41c10b5f96eaf369
-EBUILD mpich2-1.0.8.ebuild 5950 RMD160 3878cd3f0d1fd79c5456bdf806e82361a5a70c4e SHA1 6ea41421b9b6ae5bf8d1f64f0d24524134bdb298 SHA256 9cd2044f3dd94e76c8db9a3a0498461288efdab41e4aef23352f54651ea0a628
-MISC ChangeLog 845 RMD160 942e4ec9c5e10cadebd654d9123f9ce5cec4099e SHA1 f3a4889d435f8efe39719a2ba583a566e4f129fc SHA256 7c80afe12b24a3d14617ac0122c965d0960de21ca60688b7f7602b2555c68c06
+EBUILD mpich2-1.0.8-r1.ebuild 5546 RMD160 5332d8b0fa9844f195e246ca6b54619e9e01b318 SHA1 10e4ca39b6caa5b73726450bb40023dba2913260 SHA256 fcf5b454a7013c0efd450da574563e808dcd76ef5971eb0d50366362e92cbbc5
+MISC ChangeLog 1129 RMD160 ada40eabad0ac9f9bf6d5b7460c58826525521ca SHA1 1d3eab1db8f90d2bd7b86c28069597ab4b56f3eb SHA256 2f0d758c46f0738a27a023c14f4d0104d61c8afbe52aa6939c6f0a3d308dec01
 MISC metadata.xml 468 RMD160 98d955b7fd33a5b54c618424df4bc1237bb91a21 SHA1 eb055936e1a4ecafa846c1b7be6bc8c96d503ba1 SHA256 9516aa2c4536c5bc0555b42af1019a82e0f027ba8e52c0c46bcb5ee3fff8a765
diff --git a/sys-cluster/mpich2/files/mpich2-1.0.8-mpdconf-env.patch b/sys-cluster/mpich2/files/mpich2-1.0.8-mpdconf-env.patch
index f29682ad9..af3bbb239 100644
--- a/sys-cluster/mpich2/files/mpich2-1.0.8-mpdconf-env.patch
+++ b/sys-cluster/mpich2/files/mpich2-1.0.8-mpdconf-env.patch
@@ -1,7 +1,7 @@
-diff -urN mpich2-1.0.8/src/pm/mpd/Makefile.in mpich2-1.0.8_p/src/pm/mpd/Makefile.in
---- mpich2-1.0.8/src/pm/mpd/Makefile.in	2008-11-01 16:55:07.409787116 -0400
-+++ mpich2-1.0.8_p/src/pm/mpd/Makefile.in	2008-11-04 20:37:19.510506041 -0500
-@@ -78,7 +78,7 @@
+diff -urN a/mpich2-1.0.8/src/pm/mpd/Makefile.in b/mpich2-1.0.8/src/pm/mpd/Makefile.in
+--- a/mpich2-1.0.8/src/pm/mpd/Makefile.in	2008-09-17 16:40:53.000000000 -0400
++++ b/mpich2-1.0.8/src/pm/mpd/Makefile.in	2009-04-01 16:38:02.236018295 -0400
+@@ -74,7 +74,7 @@
  	$(C_LINK) -o mpdroot ${mpdroot_OBJECTS} $(LIBS)
  
  mpdroot.o: ${srcdir}/mpdroot.c ${srcdir}/mpdroot.h mpdconf.h
@@ -10,19 +10,21 @@ diff -urN mpich2-1.0.8/src/pm/mpd/Makefile.in mpich2-1.0.8_p/src/pm/mpd/Makefile
  
  # The following lines provide the right libraries for all example programs
  .c:
-@@ -136,7 +136,10 @@
- 	fi
+@@ -128,8 +128,11 @@
+ 	@echo "copying python files/links into " $(DESTDIR)${bindir}
  	-@for cmd in ${PYTHON_SOURCE} ; do \
  	    if [ ! -s $(srcdir)/$$cmd.py ] ; then continue ; fi ; \
 -	    sed -e 's#/usr/bin/env python.*#/usr/bin/env ${PYTHON}#' ${srcdir}/$$cmd.py > $(DESTDIR)${bindir}/temp$$cmd.py ; \
+-	    ${INSTALL} -m 755 $(DESTDIR)${bindir}/temp$$cmd.py $(DESTDIR)${bindir}/$$cmd.py; \
 +	    sed \
 +			-e 's#/usr/bin/env python.*#/usr/bin/env ${PYTHON}#' \
 +			-e 's,/etc/mpd.conf,@sysconfdir@/mpd.conf,g' \
 +			${srcdir}/$$cmd.py > $(DESTDIR)${bindir}/temp$$cmd.py ; \
- 	    ${INSTALL} -m 755 $(DESTDIR)${bindir}/temp$$cmd.py $(DESTDIR)${PYTHONDIR}/$$cmd.py; \
++		${INSTALL} -m 755 $(DESTDIR)${bindir}/temp$$cmd.py $(DESTDIR)${bindir}/$$cmd.py; \
  	    ( rm -f $(DESTDIR)${bindir}/temp$$cmd.py >/dev/null 2>&1 || exit 0 ) ; \
  	done
-@@ -218,7 +221,7 @@
+ 	-@cd $(DESTDIR)${bindir} && rm -f mpd
+@@ -210,7 +213,7 @@
  
  mpich2-mpdroot.o: ${srcdir}/mpdroot.c ${srcdir}/mpdroot.h mpdconf.h
  	${INSTALL} -m 644 ${srcdir}/mpdroot.c mpich2-mpdroot.c
@@ -31,21 +33,23 @@ diff -urN mpich2-1.0.8/src/pm/mpd/Makefile.in mpich2-1.0.8_p/src/pm/mpd/Makefile
  	rm -f mpich2-mpdroot.c
  
  # A special alternate installation target when using multiple process managers
-@@ -238,7 +241,10 @@
- 	fi
+@@ -226,8 +229,11 @@
+ 	fi   
  	for cmd in ${PYTHON_SOURCE} ; do \
  	    if [ ! -s $(srcdir)/$$cmd.py ] ; then continue ; fi ; \
 -	    sed -e 's#/usr/bin/env python.*#/usr/bin/env ${PYTHON}#' ${srcdir}/$$cmd.py > $(DESTDIR)${bindir}/temp$$cmd.py ; \
-+	    sed \
+-	    ${INSTALL} -m 755 $(DESTDIR)${bindir}/temp$$cmd.py $(DESTDIR)${bindir}/$$cmd.py; \
++		sed \
 +			-e 's#/usr/bin/env python.*#/usr/bin/env ${PYTHON}#' \
 +			-e 's,/etc/mpd.conf,@sysconfdir@/mpd.conf,g' \
 +			${srcdir}/$$cmd.py > $(DESTDIR)${bindir}/temp$$cmd.py ; \
- 	    ${INSTALL} -m 755 $(DESTDIR)${bindir}/temp$$cmd.py $(DESTDIR)${PYTHONDIR}/$$cmd.py; \
++		${INSTALL} -m 755 $(DESTDIR)${bindir}/temp$$cmd.py $(DESTDIR)${bindir}/$$cmd.py; \
  	    ( rm -f $(DESTDIR)${bindir}/temp$$cmd.py >/dev/null 2>&1 || exit 0 ) ; \
  	done
-diff -urN mpich2-1.0.8/src/pm/mpd/mpdlib.py mpich2-1.0.8_p/src/pm/mpd/mpdlib.py
---- mpich2-1.0.8/src/pm/mpd/mpdlib.py	2007-11-08 18:47:44.000000000 -0500
-+++ mpich2-1.0.8_p/src/pm/mpd/mpdlib.py	2008-11-04 20:40:36.812894529 -0500
+ 	cd $(DESTDIR)${bindir} && rm -f mpd
+diff -urN a/mpich2-1.0.8/src/pm/mpd/mpdlib.py b/mpich2-1.0.8/src/pm/mpd/mpdlib.py
+--- a/mpich2-1.0.8/src/pm/mpd/mpdlib.py	2007-11-08 18:47:44.000000000 -0500
++++ b/mpich2-1.0.8/src/pm/mpd/mpdlib.py	2009-04-01 16:35:08.899627072 -0400
 @@ -1341,11 +1341,11 @@
              if os.environ.has_key(k):
                  self[('env',k)] = os.environ[k]
@@ -60,9 +64,9 @@ diff -urN mpich2-1.0.8/src/pm/mpd/mpdlib.py mpich2-1.0.8_p/src/pm/mpd/mpdlib.py
              parmsRCFilename = os.path.join(os.environ['HOME'],'.mpd.conf')
          elif os.environ.has_key('HOMEPATH'):    # e.g. win32
              parmsRCFilename = os.path.join(os.environ['HOMEPATH'],'.mpd.conf')
-diff -urN mpich2-1.0.8/src/pm/mpd/mpdroot.c mpich2-1.0.8_p/src/pm/mpd/mpdroot.c
---- mpich2-1.0.8/src/pm/mpd/mpdroot.c	2007-11-02 18:50:19.000000000 -0400
-+++ mpich2-1.0.8_p/src/pm/mpd/mpdroot.c	2008-11-07 13:45:10.560017904 -0500
+diff -urN a/mpich2-1.0.8/src/pm/mpd/mpdroot.c b/mpich2-1.0.8/src/pm/mpd/mpdroot.c
+--- a/mpich2-1.0.8/src/pm/mpd/mpdroot.c	2007-11-02 18:50:19.000000000 -0400
++++ b/mpich2-1.0.8/src/pm/mpd/mpdroot.c	2009-04-01 16:35:08.899627072 -0400
 @@ -19,6 +19,7 @@
      struct passwd *pwent;
      char input_line[NAME_LEN+1], secretword[NAME_LEN+1];
diff --git a/sys-cluster/mpich2/files/mpich2-1.0.8-site-packages-py.patch b/sys-cluster/mpich2/files/mpich2-1.0.8-site-packages-py.patch
deleted file mode 100644
index a3e894e74..000000000
--- a/sys-cluster/mpich2/files/mpich2-1.0.8-site-packages-py.patch
+++ /dev/null
@@ -1,161 +0,0 @@
-diff -urN mpich2-1.0.8/src/pm/mpd/Makefile.in mpich2-1.0.8_p/src/pm/mpd/Makefile.in
---- mpich2-1.0.8/src/pm/mpd/Makefile.in	2008-09-17 16:40:53.000000000 -0400
-+++ mpich2-1.0.8_p/src/pm/mpd/Makefile.in	2008-11-01 13:17:08.518285830 -0400
-@@ -20,6 +20,10 @@
- INSTALL   = @INSTALL@
- CFLAGS    = @CFLAGS@
- 
-+LIBDIRNAME = `echo @libdir@ | sed 's:.*@prefix@/::'`
-+PYTHONDIR  = ${prefix}/${LIBDIRNAME}/${PYTHON}/site-packages/mpich2
-+PYTHONLINK = ../${LIBDIRNAME}/${PYTHON}/site-packages/mpich2
-+
- C_COMPILE = ${CC} ${INCLUDES} ${CFLAGS} ${COPTIONS}
- C_LINK	  = ${CLINKER} ${CFLAGS} ${COPTIONS} ${LDFLAGS}
- 
-@@ -125,29 +129,33 @@
-         else \
- 	    ${INSTALL} -m  755 mpdroot $(DESTDIR)${bindir}/mpdroot ;\
- 	fi
--	@echo "copying python files/links into " $(DESTDIR)${bindir}
-+	@echo "copying python files/links into " $(DESTDIR)${PYTHONDIR}
-+	@if [ ! -d $(DESTDIR)${PYTHONDIR} ] ; then \
-+		echo "mkdir -p $(DESTDIR)${PYTHONDIR} " ;\
-+		mkdir -p $(DESTDIR)${PYTHONDIR} ; \
-+	fi
- 	-@for cmd in ${PYTHON_SOURCE} ; do \
- 	    if [ ! -s $(srcdir)/$$cmd.py ] ; then continue ; fi ; \
- 	    sed -e 's#/usr/bin/env python.*#/usr/bin/env ${PYTHON}#' ${srcdir}/$$cmd.py > $(DESTDIR)${bindir}/temp$$cmd.py ; \
--	    ${INSTALL} -m 755 $(DESTDIR)${bindir}/temp$$cmd.py $(DESTDIR)${bindir}/$$cmd.py; \
-+	    ${INSTALL} -m 755 $(DESTDIR)${bindir}/temp$$cmd.py $(DESTDIR)${PYTHONDIR}/$$cmd.py; \
- 	    ( rm -f $(DESTDIR)${bindir}/temp$$cmd.py >/dev/null 2>&1 || exit 0 ) ; \
- 	done
- 	-@cd $(DESTDIR)${bindir} && rm -f mpd
--	-@cd $(DESTDIR)${bindir} && @LN_S@ mpd.py mpd
-+	-@cd $(DESTDIR)${bindir} && @LN_S@ ${PYTHONLINK}/mpd.py mpd
- 	-@cd $(DESTDIR)${bindir} && rm -f mpdboot
--	-@cd $(DESTDIR)${bindir} && @LN_S@ mpdboot.py mpdboot
-+	-@cd $(DESTDIR)${bindir} && @LN_S@ ${PYTHONLINK}/mpdboot.py mpdboot
- 	-@for cmd in ${CMDS} ; do \
- 	    ( cd $(DESTDIR)${bindir} && rm -f $$cmd ; ) ; \
--	    ( cd $(DESTDIR)${bindir} && @LN_S@ $$cmd.py $$cmd ; ) \
-+	    ( cd $(DESTDIR)${bindir} && @LN_S@ ${PYTHONLINK}/$$cmd.py $$cmd ; ) \
- 	done
- 	-@( rm -f $(DESTDIR)${bindir}/mpdrun >/dev/null 2>&1 || exit 0 )
--	-@( rm -f $(DESTDIR)${bindir}/mpdrun.py >/dev/null 2>&1 || exit 0 )
-+	-@( rm -f $(DESTDIR)${PYTHONDIR}/mpdrun.py >/dev/null 2>&1 || exit 0 )
- 	-@( rm -f $(DESTDIR)${bindir}/mpirun >/dev/null 2>&1 || exit 0 )
--	-@( rm -f $(DESTDIR)${bindir}/mpirun.py >/dev/null 2>&1 || exit 0 )
--	-@cd $(DESTDIR)${bindir} && @LN_S@ mpiexec mpdrun
--	-@cd $(DESTDIR)${bindir} && @LN_S@ mpiexec.py mpdrun.py
--	-@cd $(DESTDIR)${bindir} && @LN_S@ mpiexec mpirun
--	-@cd $(DESTDIR)${bindir} && @LN_S@ mpiexec.py mpirun.py
-+	-@( rm -f $(DESTDIR)${PYTHONDIR}/mpirun.py >/dev/null 2>&1 || exit 0 )
-+	-@cd $(DESTDIR)${bindir} && @LN_S@ ${PYTHONLINK}/mpiexec.py mpdrun
-+	-@cd $(DESTDIR)${bindir} && @LN_S@ ${PYTHONLINK}/mpiexec.py mpdrun.py
-+	-@cd $(DESTDIR)${bindir} && @LN_S@ ${PYTHONLINK}/mpiexec.py mpirun
-+	-@cd $(DESTDIR)${bindir} && @LN_S@ ${PYTHONLINK}/mpiexec.py mpirun.py
- 	-@if [ "${DO_MTV}" = "yes" ] ; then \
- 	    ${INSTALL} -m 755 mtv.so $(DESTDIR)${bindir}/mtv.so ;\
- 	fi
-@@ -166,43 +174,43 @@
- 	-rm -f $(DESTDIR)${bindir}/mpdroot
- 	-rm -f $(DESTDIR)${bindir}/Zeroconf.py
- 	-rm -f $(DESTDIR)${bindir}/mpd
--	-rm -f $(DESTDIR)${bindir}/mpd.py
-+	-rm -f $(DESTDIR)${PYTHONDIR}/mpd.py
- 	-rm -f $(DESTDIR)${bindir}/mpdallexit
--	-rm -f $(DESTDIR)${bindir}/mpdallexit.py
-+	-rm -f $(DESTDIR)${PYTHONDIR}/mpdallexit.py
- 	-rm -f $(DESTDIR)${bindir}/mpdboot
--	-rm -f $(DESTDIR)${bindir}/mpdboot.py
-+	-rm -f $(DESTDIR)${PYTHONDIR}/mpdboot.py
- 	-rm -f $(DESTDIR)${bindir}/mpdcheck
--	-rm -f $(DESTDIR)${bindir}/mpdcheck.py
--	-rm -f $(DESTDIR)${bindir}/mpdchkpyver.py
-+	-rm -f $(DESTDIR)${PYTHONDIR}/mpdcheck.py
-+	-rm -f $(DESTDIR)${PYTHONDIR}/mpdchkpyver.py
- 	-rm -f $(DESTDIR)${bindir}/mpdcleanup
--	-rm -f $(DESTDIR)${bindir}/mpdcleanup.py
-+	-rm -f $(DESTDIR)${PYTHONDIR}/mpdcleanup.py
- 	-rm -f $(DESTDIR)${bindir}/mpdexit
--	-rm -f $(DESTDIR)${bindir}/mpdexit.py
--	-rm -f $(DESTDIR)${bindir}/mpdgdbdrv.py
-+	-rm -f $(DESTDIR)${PYTHONDIR}/mpdexit.py
-+	-rm -f $(DESTDIR)${PYTHONDIR}/mpdgdbdrv.py
- 	-rm -f $(DESTDIR)${bindir}/mpdhelp
--	-rm -f $(DESTDIR)${bindir}/mpdhelp.py
-+	-rm -f $(DESTDIR)${PYTHONDIR}/mpdhelp.py
- 	-rm -f $(DESTDIR)${bindir}/mpdkilljob
--	-rm -f $(DESTDIR)${bindir}/mpdkilljob.py
--	-rm -f $(DESTDIR)${bindir}/mpdlib.py
--	-rm -f $(DESTDIR)${bindir}/mpdlib.pyc
-+	-rm -f $(DESTDIR)${PYTHONDIR}/mpdkilljob.py
-+	-rm -f $(DESTDIR)${PYTHONDIR}/mpdlib.py
-+	-rm -f $(DESTDIR)${PYTHONDIR}/mpdlib.pyc
- 	-rm -f $(DESTDIR)${bindir}/mpdlistjobs
--	-rm -f $(DESTDIR)${bindir}/mpdlistjobs.py
--	-rm -f $(DESTDIR)${bindir}/mpdman.py
--	-rm -f $(DESTDIR)${bindir}/mpdman.pyc
-+	-rm -f $(DESTDIR)${PYTHONDIR}/mpdlistjobs.py
-+	-rm -f $(DESTDIR)${PYTHONDIR}/mpdman.py
-+	-rm -f $(DESTDIR)${PYTHONDIR}/mpdman.pyc
- 	-rm -f $(DESTDIR)${bindir}/mpdringtest
--	-rm -f $(DESTDIR)${bindir}/mpdringtest.py
-+	-rm -f $(DESTDIR)${PYTHONDIR}/mpdringtest.py
- 	-rm -f $(DESTDIR)${bindir}/mpdrun
--	-rm -f $(DESTDIR)${bindir}/mpdrun.py
-+	-rm -f $(DESTDIR)${PYTHONDIR}/mpdrun.py
- 	-rm -f $(DESTDIR)${bindir}/mpdsigjob
--	-rm -f $(DESTDIR)${bindir}/mpdsigjob.py
-+	-rm -f $(DESTDIR)${PYTHONDIR}/mpdsigjob.py
- 	-rm -f $(DESTDIR)${bindir}/mpdtrace
--	-rm -f $(DESTDIR)${bindir}/mpdtrace.py
-+	-rm -f $(DESTDIR)${PYTHONDIR}/mpdtrace.py
- 	-rm -f $(DESTDIR)${bindir}/mpecc.in
- 	-rm -f $(DESTDIR)${bindir}/mpefc.in
- 	-rm -f $(DESTDIR)${bindir}/mpiexec
--	-rm -f $(DESTDIR)${bindir}/mpiexec.py
-+	-rm -f $(DESTDIR)${PYTHONDIR}/mpiexec.py
- 	-rm -f $(DESTDIR)${bindir}/mpirun
--	-rm -f $(DESTDIR)${bindir}/mpirun.py
-+	-rm -f $(DESTDIR)${PYTHONDIR}/mpirun.py
- 
- mpich2-mpdroot: mpich2-mpdroot.o
- 	$(C_LINK) -o mpich2-mpdroot mpich2-mpdroot.o $(LIBS)
-@@ -224,25 +232,29 @@
- 	    echo "mkdir -p $(DESTDIR)${bindir} " ;\
- 	    mkdir -p $(DESTDIR)${bindir} ;\
- 	fi   
-+	@if [ ! -d $(DESTDIR)${PYTHONDIR} ] ; then \
-+		echo "mkdir -p $(DESTDIR)${PYTHONDIR} " ;\
-+		mkdir -p $(DESTDIR)${PYTHONDIR} ; \
-+	fi
- 	for cmd in ${PYTHON_SOURCE} ; do \
- 	    if [ ! -s $(srcdir)/$$cmd.py ] ; then continue ; fi ; \
- 	    sed -e 's#/usr/bin/env python.*#/usr/bin/env ${PYTHON}#' ${srcdir}/$$cmd.py > $(DESTDIR)${bindir}/temp$$cmd.py ; \
--	    ${INSTALL} -m 755 $(DESTDIR)${bindir}/temp$$cmd.py $(DESTDIR)${bindir}/$$cmd.py; \
-+	    ${INSTALL} -m 755 $(DESTDIR)${bindir}/temp$$cmd.py $(DESTDIR)${PYTHONDIR}/$$cmd.py; \
- 	    ( rm -f $(DESTDIR)${bindir}/temp$$cmd.py >/dev/null 2>&1 || exit 0 ) ; \
- 	done
- 	cd $(DESTDIR)${bindir} && rm -f mpd
--	cd $(DESTDIR)${bindir} && @LN_S@ mpd.py mpd
-+	cd $(DESTDIR)${bindir} && @LN_S@ ${PYTHONLINK}/mpd.py mpd
- 	cd $(DESTDIR)${bindir} && rm -f mpdboot
--	cd $(DESTDIR)${bindir} && @LN_S@ mpdboot.py mpdboot
-+	cd $(DESTDIR)${bindir} && @LN_S@ ${PYTHONLINK}/mpdboot.py mpdboot
- 	for cmd in ${CMDS} ; do \
- 	    if [ $$cmd = "mpiexec" ] ; then continue ; fi ; \
- 	    ( cd $(DESTDIR)${bindir} && rm -f $$cmd ; ) ; \
--	    ( cd $(DESTDIR)${bindir} && @LN_S@ $$cmd.py $$cmd ; ) \
-+	    ( cd $(DESTDIR)${bindir} && @LN_S@ )${PYTHONLINK}/$$cmd.py $$cmd ; ) \
- 	done
--	( rm -f $(DESTDIR)${bindir}/mpdrun >/dev/null 2>&1 || exit 0 )
-+	( rm -f $(DESTDIR)${PYTHONDIR}/mpdrun >/dev/null 2>&1 || exit 0 )
- 	( rm -f $(DESTDIR)${bindir}/mpdrun.py >/dev/null 2>&1 || exit 0 )
--	mv -f $(DESTDIR)${bindir}/mpiexec.py $(DESTDIR)${bindir}/mpiexec.mpd
--	cd $(DESTDIR)${bindir} && @LN_S@ mpiexec.mpd mpdrun
-+	mv -f $(DESTDIR)${PYTHONDIR}/mpiexec.py $(DESTDIR)${PYTHONDIR}/mpiexec.mpd
-+	cd $(DESTDIR)${bindir} && @LN_S@ )${PYTHONLINK}/mpiexec.mpd mpdrun
- 
- # Empty dependencies target (MPICH2 wants this target)
- dependencies:
diff --git a/sys-cluster/mpich2/mpich2-1.0.8.ebuild b/sys-cluster/mpich2/mpich2-1.0.8-r1.ebuild
index a9596795c..e16deb49d 100644
--- a/sys-cluster/mpich2/mpich2-1.0.8.ebuild
+++ b/sys-cluster/mpich2/mpich2-1.0.8-r1.ebuild
@@ -2,7 +2,7 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-inherit python eutils fortran mpi
+inherit eutils fortran mpi
 
 DESCRIPTION="MPICH2 - A portable MPI implementation"
 HOMEPAGE="http://www-unix.mcs.anl.gov/mpi/mpich2"
@@ -52,8 +52,6 @@ pkg_setup() {
 	else
 		MPD_CONF_FILE_DIR=/etc/${PN}
 	fi
-
-	python_version
 }
 
 src_unpack() {
@@ -69,11 +67,6 @@ src_unpack() {
 	sed -i 's/-fpic/-fPIC/g' \
 		$(grep -lr -e '-fpic' "${S}"/) || die "failed to change -fpic to -fPIC"
 
-	# Put python files in site-packages where they belong.
-	# This isn't the prettiest little patch, but it does
-	# move python files out of /usr/bin/
-	epatch "${FILESDIR}"/${P}-site-packages-py.patch
-
 	# Respect the env var MPD_CONF_FILE
 	# TODO:  Send upstream
 	epatch "${FILESDIR}"/${P}-mpdconf-env.patch
@@ -195,15 +188,15 @@ src_install() {
 		mv "${D}"/${d}/usr/share/doc/www*/* "${D}"/${d}/usr/share/doc/${PF}/www/
 	fi
 
-	#TODO: Need to handle python path here if mpi_classed?
 	cp "${FILESDIR}"/${PN}.envd "${T}"/
 	sed -i "s,@MPD_CONF_FILE_DIR@,${MPD_CONF_FILE_DIR}," \
-		"${T}"/${PN}.envd
+		"${T}"/${PN}.envd || die
 
 	if mpi_classed; then
+		# TODO:  This breaks down with more than one mpich2 installed.
 		newenvd "${T}"/${PN}.envd 25mpich2-$(mpi_class)
 	else
-		newenvd "${FILESDIR}"/${PN}.envd 25mpich2
+		newenvd "${T}"/${PN}.envd 25mpich2
 	fi
 
 	mpi_imp_add_eselect
@@ -214,14 +207,8 @@ pkg_postinst() {
 	chown root:root "${ROOT}"${MPD_CONF_FILE_DIR}/mpd.conf
 	chmod 600 "${ROOT}"${MPD_CONF_FILE_DIR}/mpd.conf
 
-	python_mod_optimize $(mpi_root)/usr/$(get_libdir)/python${PYVER}/site-packages/${PN}
 	elog ""
 	elog "MPE2 has been removed from this ebuild and now stands alone"
 	elog "as sys-cluster/mpe2."
 	elog ""
 }
-
-pkg_postrm() {
-	python_mod_cleanup $(mpi_root)/usr/$(get_libdir)/python${PYVER}/site-packages/${PN}
-}
-