(#212054) New package: ARP/wARP is a software for improvement and interpretation of crystallographic electron density maps.

Package-Manager: portage-2.2_rc5/cvs/Linux 2.6.26 x86_64

6 files changed, 334 insertions, 0 deletions

diff --git a/sci-chemistry/arp-warp-bin/ChangeLog b/sci-chemistry/arp-warp-bin/ChangeLog
new file mode 100644
index 000000000000..927eceb2dff0
--- /dev/null
+++ b/sci-chemistry/arp-warp-bin/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-chemistry/arp-warp-bin
+# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/arp-warp-bin/ChangeLog,v 1.1 2008/08/04 00:11:54 dberkholz Exp $
+
+*arp-warp-bin-7.0.1-r1 (04 Aug 2008)
+
+  04 Aug 2008; Donnie Berkholz <dberkholz@gentoo.org>;
+  +files/7.0.1-setup.patch, +files/7.0.1-source-ccp4-if-needed.patch,
+  +metadata.xml, +arp-warp-bin-7.0.1-r1.ebuild:
+  (#212054) New package: ARP/wARP is a software for improvement and
+  interpretation of crystallographic electron density maps.
+
diff --git a/sci-chemistry/arp-warp-bin/Manifest b/sci-chemistry/arp-warp-bin/Manifest
new file mode 100644
index 000000000000..c35d611fffd2
--- /dev/null
+++ b/sci-chemistry/arp-warp-bin/Manifest
@@ -0,0 +1,16 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+AUX 7.0.1-setup.patch 6330 RMD160 eb59c2023f3d023a1c50322960c4d3ee7d85b414 SHA1 7e4f8c375faea911dcf8787f735eeeca658b273b SHA256 f1136bb00c60194a504f0bf718733a13d5bea88fd88231a553f82993f97928da
+AUX 7.0.1-source-ccp4-if-needed.patch 1334 RMD160 e1c04014322a4406eb6421c12d9d97266e294a6b SHA1 0e7c8259f8996ebd13c3df1d2b1f894d7418a85b SHA256 0a554438fa7ba994762b463b7340af5f5cab3177c62e7632a313830d92228205
+DIST arp_warp_7.0.1.tar.gz 212443160 RMD160 b6b821a4135520456f489cb96e650b3be61c4892 SHA1 957ddb8ad5dde9556a6306643bb638288b144ca6 SHA256 368cff316fd05ca98937f2709b0ef8b391bc71697f61c7474c4681c99b24e677
+EBUILD arp-warp-bin-7.0.1-r1.ebuild 2621 RMD160 a0fb33550e2d4f12a0d139f0ca79b5d82be17f70 SHA1 bebbf0549535733e11418bfca4965840184381d3 SHA256 939f00ca5b6f21a90bb8424efd07469da0b20b745f2093121ff1a3ffd2e805c6
+MISC ChangeLog 568 RMD160 b849b1d809bae8ca0d2ba7b256bd3cba2d994393 SHA1 3bf0fa3bd1680c8421ee34930c2e111e207e2709 SHA256 e1ccac360e1b9a1da7a98e08b3c64612914c53de67faac61089b1e386c37d271
+MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.9 (GNU/Linux)
+
+iEYEARECAAYFAkiWSVUACgkQXVaO67S1rtuLMQCeJ/qalmgmCjPUsnyjTB1voU0H
+Ih8AoJfkenzAK346EG2qggWci+AAvOK4
+=n2vW
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/arp-warp-bin/arp-warp-bin-7.0.1-r1.ebuild b/sci-chemistry/arp-warp-bin/arp-warp-bin-7.0.1-r1.ebuild
new file mode 100644
index 000000000000..fd3e686f9a17
--- /dev/null
+++ b/sci-chemistry/arp-warp-bin/arp-warp-bin-7.0.1-r1.ebuild
@@ -0,0 +1,87 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/arp-warp-bin/arp-warp-bin-7.0.1-r1.ebuild,v 1.1 2008/08/04 00:11:54 dberkholz Exp $
+
+inherit eutils python
+
+MY_P="arp_warp_${PV}"
+DESCRIPTION="ARP/wARP is a software for improvement and interpretation of crystallographic electron density maps"
+SRC_URI="${MY_P}.tar.gz"
+HOMEPAGE="http://www.embl-hamburg.de/ARP/"
+LICENSE="ArpWarp"
+RESTRICT="fetch"
+SLOT="0"
+KEYWORDS="-* ~amd64 ~x86"
+IUSE=""
+RDEPEND="app-shells/tcsh
+	 >=sci-chemistry/ccp4-6
+	 sys-apps/gawk
+	 >=dev-lang/python-2.4"
+DEPEND=""
+S="${WORKDIR}/${MY_P}"
+
+pkg_nofetch(){
+	elog "Fill out the form at http://www.embl-hamburg.de/ARP/"
+	elog "and place ${A} in ${DISTDIR}"
+}
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+	epatch "${FILESDIR}"/${PV}-setup.patch
+	epatch "${FILESDIR}"/${PV}-source-ccp4-if-needed.patch
+}
+
+src_install(){
+	python_version
+	m_type=$(uname -m)
+	os_type=$(uname)
+
+	insinto /opt/${PN}/byte-code/python-${PYVER}
+	doins "${S}"/flex-wARP-src-261/*py
+
+	exeinto /opt/${PN}/bin/bin-${m_type}-${os_type}
+	doexe "${S}"/bin/bin-${m_type}-${os_type}/* && \
+	doexe "${S}"/share/*sh || die
+
+	insinto /opt/${PN}/bin/bin-${m_type}-${os_type}
+	doins "${S}"/share/*{gif,XYZ,bash,csh,dat,lib,tbl,llh} || die
+
+	insinto /etc/profile.d/
+	newins "${S}"/share/arpwarp_setup_base.csh 90arpwarp_setup.csh && \
+	newins "${S}"/share/arpwarp_setup_base.bash 90arpwarp_setup.sh || die
+
+	dodoc "${S}"/README
+	dohtml -r "${S}"/manual/*
+	insinto /usr/share/doc/${PF}
+	doins -r "${S}"/{examples,ARP_wARP_CCP4I6.tar.gz}
+}
+
+pkg_postinst(){
+	python_mod_optimize "${ROOT}"/opt/${PN}/byte-code/python-${PYVER}
+
+	testcommand=$(echo 3 2 | awk '{printf"%3.1f",$1/$2}')
+	if [ $testcommand == "1,5" ];then
+	  ewarn "*** ERROR ***"
+	  ewarn "   3/2=" $testcommand
+	  ewarn "Invalid decimal separator (must be ".")"
+	  ewarn "You need to set this correctly!!!"
+	  ewarn
+	  ewarn "One way of setting the decimal separator is:"
+	  ewarn "setenv LC_NUMERIC C' in your .cshrc file"
+	  ewarn "\tor"
+	  ewarn "export LC_NUMERIC=C' in your .bashrc file"
+	  ewarn "Otherwise please consult your system manager"
+	  epause 10
+	fi
+
+	grep -q sse2 /proc/cpuinfo || einfo "The CPU is lacking SSE2! You should use the cluster at EMBL-Hamburg."
+	einfo
+	elog "The ccp4 interface file could be found in /usr/share/doc/"${P}
+	elog "To install, run ccp4i as root, navigate to System Administration,"
+	elog "Install/uninstall tasks, then choose ARP_wARP_CCP4I6.tar.gz."
+}
+
+pkg_postrm() {
+	python_mod_cleanup "${ROOT}"/opt/${PN}/byte-code/python-${PYVER}
+}
diff --git a/sci-chemistry/arp-warp-bin/files/7.0.1-setup.patch b/sci-chemistry/arp-warp-bin/files/7.0.1-setup.patch
new file mode 100644
index 000000000000..72bd06503deb
--- /dev/null
+++ b/sci-chemistry/arp-warp-bin/files/7.0.1-setup.patch
@@ -0,0 +1,170 @@
+diff -Nu -Nu -uarN arp_warp_7.0.1.orig/share/arpwarp_setup_base.bash arp_warp_7.0.1/share/arpwarp_setup_base.bash
+--- arp_warp_7.0.1.orig/share/arpwarp_setup_base.bash	2007-10-21 21:46:13.000000000 +0200
++++ arp_warp_7.0.1/share/arpwarp_setup_base.bash	2008-04-06 13:33:05.000000000 +0200
+@@ -13,10 +13,10 @@
+     identifier=${nameprocessor}'-'${namesystem}
+ fi
+ #
+-arpwarphome="$1X"
++arpwarphome="/opt/arp-warp-bin"
+ #
+ export warpbin=${arpwarphome}/bin/bin-${identifier}
+-export warpdoc=${arpwarphome}/manual
++export warpdoc=/usr/share/doc/arp-warp-bin-7.0.1/html/
+ export PATH=${warpbin}:${PATH}
+ #
+ testccp='0'
+@@ -49,7 +49,7 @@
+     fi
+ 
+ ##    2. Complement by other potential places for python :
+-    search_list="${search_list} /usr/local/bin/python /usr/bin/python"
++    search_list="${search_list} /usr/bin/python"
+     flex_wARP_python="/dev/null"
+ 
+ ##    3. Pick up the first one of the list which seems reasonable :
+@@ -73,30 +73,6 @@
+             export flex_wARP_bin=${HOME}/.flex-wARP/python-${pythonvrs1}.${pythonvrs2}
+             break
+         fi
+-#        3.c Otherwise, we should be able to create the byte-code using the python.
+-        /bin/mkdir -p ${arpwarphome}/byte-code/python-${pythonvrs1}.${pythonvrs2} 1> /dev/null 2>&1
+-        if [ 0 != $? ] ; then
+-            /bin/mkdir -p ${HOME}/.flex-wARP/python-${pythonvrs1}.${pythonvrs2} 1> /dev/null 2>&1
+-            export flex_wARP_bin=${HOME}/.flex-wARP/python-${pythonvrs1}.${pythonvrs2}
+-        else
+-            export flex_wARP_bin=${arpwarphome}/byte-code/python-${pythonvrs1}.${pythonvrs2}
+-        fi
+-        pushd ${flex_wARP_bin} 1> /dev/null 2>&1
+-        if [ 0 != $? ] ; then 
+-            export flex_wARP_bin=${HOME}/.flex-wARP/python-${pythonvrs1}.${pythonvrs2}
+-            /bin/mkdir -p ${flex_wARP_bin} 1> /dev/null 2>&1
+-            pushd ${flex_wARP_bin} 1> /dev/null 2>&1
+-        fi
+-        /bin/cp -p ${arpwarphome}/flex-wARP-src/*.py .
+-        ${python_to_test} ./compile.py
+-        /bin/rm -f *.py
+-        popd 1> /dev/null 2>&1
+-        if [ -e ${flex_wARP_bin}/CPyWARP.pyc ] ; then
+-            export flex_wARP_python=${python_to_test}
+-            echo "Created a new set of flex-wARP byte code in the directory :"
+-            echo "  '${flex_wARP_bin}'"
+-            break
+-        fi
+     done
+ ##    4. If nothing is available, print out a message.
+     if [ "/dev/null" != ${flex_wARP_python} ] ; then
+@@ -107,6 +83,7 @@
+         echo "WARNING while setting up ARP/wARP"
+         echo "No valid 'python' command was found"
+         echo "flex-warp ('ARP/wARP Expert System' in the GUI) will not be available."
++	echo "Did you upgrade your python? Reemerge ArpWarp!"
+         echo
+         export flex_wARP_warpbin="Unavailable"
+         export flex_wARP_cbin="Unavailable"
+@@ -115,17 +92,3 @@
+     fi
+ fi
+ 
+-#
+-# Setting up library path for SGI
+-if [[ "${namesystem}" = 'IRIX64' || "${namesystem}" = 'IRIX' ]]; then
+-    if test "$LD_LIBRARY_PATH"; then
+-        export LD_LIBRARY_PATH=${warpbin}:${LD_LIBRARY_PATH}
+-    else
+-        export LD_LIBRARY_PATH=${warpbin}
+-    fi
+-fi
+-#   echo
+-#   echo 'ARP/wARP Version 7.0.1 has been setup'
+-#
+-
+-
+diff -Nu -Nu -uarN arp_warp_7.0.1.orig/share/arpwarp_setup_base.csh arp_warp_7.0.1/share/arpwarp_setup_base.csh
+--- arp_warp_7.0.1.orig/share/arpwarp_setup_base.csh	2007-10-21 21:46:13.000000000 +0200
++++ arp_warp_7.0.1/share/arpwarp_setup_base.csh	2008-04-06 13:32:48.000000000 +0200
+@@ -13,10 +13,10 @@
+     set identifier = ${nameprocessor}'-'${namesystem}
+ endif
+ #
+-set arpwarphome = '$1X'
++set arpwarphome = '/opt/arp-warp-bin'
+ #
+ setenv warpbin ${arpwarphome}/bin/bin-${identifier}
+-setenv warpdoc ${arpwarphome}/manual
++setenv warpdoc /usr/share/doc/arp-warp-bin-7.0.1/html/
+ set path = ( $warpbin $path )
+ #
+ # Settings for python
+@@ -47,7 +47,7 @@
+ endif
+ 
+ ##    2. Complement by other potential places for python :
+-set search_list = "${search_list} /usr/local/bin/python /usr/bin/python"
++set search_list = "${search_list} /usr/bin/python"
+ setenv flex_wARP_python "/dev/null"
+ 
+ ##    3. Pick up the first one of the list which seems reasonable :
+@@ -71,30 +71,6 @@
+         setenv flex_wARP_bin ${HOME}/.flex-wARP/python-${pythonvrs1}.${pythonvrs2}
+         break
+     endif
+-#        3.c Otherwise, we should be able to create the byte-code using the python.
+-    /bin/mkdir -p ${arpwarphome}/byte-code/python-${pythonvrs1}.${pythonvrs2} >& /dev/null
+-    if ( 0 != $status ) then
+-        /bin/mkdir -p ${HOME}/.flex-wARP/python-${pythonvrs1}.${pythonvrs2} >& /dev/null
+-        setenv flex_wARP_bin ${HOME}/.flex-wARP/python-${pythonvrs1}.${pythonvrs2}
+-    else
+-        setenv flex_wARP_bin ${arpwarphome}/byte-code/python-${pythonvrs1}.${pythonvrs2}
+-    endif
+-    pushd ${flex_wARP_bin} >& /dev/null
+-    if ( 0 != $status ) then
+-        setenv flex_wARP_bin ${HOME}/.flex-wARP/python-${pythonvrs1}.${pythonvrs2}
+-        /bin/mkdir -p ${flex_wARP_bin} >& /dev/null
+-        pushd ${flex_wARP_bin} >& /dev/null
+-    endif
+-    /bin/cp -p ${arpwarphome}/flex-wARP-src/*.py .
+-    ${python_to_test} ./compile.py
+-    /bin/rm -f *.py
+-    popd >& /dev/null
+-    if ( -e ${flex_wARP_bin}/CPyWARP.pyc ) then
+-        setenv flex_wARP_python ${python_to_test}
+-        echo "Created a new set of flex-wARP byte code in the directory :"
+-        echo "  '${flex_wARP_bin}'"
+-        break
+-    endif
+ end
+ ##    4. If nothing is available, print out a message.
+ if ( "/dev/null" != ${flex_wARP_python} ) then
+@@ -105,22 +81,13 @@
+     echo "WARNING while setting up ARP/wARP"
+     echo "No valid 'python' command was found"
+     echo "flex-warp ('ARP/wARP Expert System' in the GUI) will not be available."
++    echo "Did you upgrade your python? Reemerge ArpWarp!"
+     echo
+     setenv flex_wARP_warpbin "Unavailable"
+     setenv flex_wARP_cbin "Unavailable"
+     setenv flex_wARP_python "/dev/null"
+     setenv flex_wARP_bin "Unavailable"
+ endif
+-
+-#
+-# Setting up library path for SGI
+-if ( ${namesystem} == 'IRIX64' || ${namesystem} == 'IRIX' ) then
+-    if ( ${?LD_LIBRARY_PATH} ) then
+-        setenv LD_LIBRARY_PATH ${warpbin}:${LD_LIBRARY_PATH}
+-    else
+-        setenv LD_LIBRARY_PATH ${warpbin}
+-    endif
+-endif
+ #
+ goto endsetup
+ #
+@@ -132,7 +99,4 @@
+ #
+ endsetup:
+ #
+-#echo
+-#echo 'ARP/wARP Version 7.0.1 has been setup'
+-#
+ 
diff --git a/sci-chemistry/arp-warp-bin/files/7.0.1-source-ccp4-if-needed.patch b/sci-chemistry/arp-warp-bin/files/7.0.1-source-ccp4-if-needed.patch
new file mode 100644
index 000000000000..ce23403d2add
--- /dev/null
+++ b/sci-chemistry/arp-warp-bin/files/7.0.1-source-ccp4-if-needed.patch
@@ -0,0 +1,44 @@
+--- share.orig/arpwarp_setup_base.bash	2008-08-03 16:50:03.000000000 -0700
++++ share/arpwarp_setup_base.bash	2008-08-03 16:51:20.000000000 -0700
+@@ -23,11 +23,14 @@
+ #
+ # Checks for CBIN variable
+ if [ "$CBIN" = "" ]; then
+-    echo
+-    echo "Cannot setup ARP/wARP"
+-    echo 'Variable $CBIN is not defined'
+-    echo "Please install CCP4 first"
+-    testccp='1'
++    source /etc/profile.d/ccp4.setup.sh
++    if [ "$CBIN" = "" ]; then
++        echo
++        echo "Cannot setup ARP/wARP"
++        echo 'Variable $CBIN is not defined'
++        echo "Please install CCP4 first"
++        testccp='1'
++    fi
+ fi
+ if [ "$testccp" = '0' ]; then
+     if [ ! -d $CBIN ]; then
+--- share.orig/arpwarp_setup_base.csh	2008-08-03 16:50:06.000000000 -0700
++++ share/arpwarp_setup_base.csh	2008-08-03 16:52:03.000000000 -0700
+@@ -22,11 +22,14 @@
+ # Settings for python
+ # Checks for CBIN variable
+ if ( ! $?CBIN ) then
+-    echo
+-    echo 'Cannot setup ARP/wARP'
+-    echo 'Variable $CBIN is not defined'
+-    echo 'Please install CCP4 first'
+-    goto errorsetup
++    source /etc/profile.d/ccp4.setup.sh
++    if ( ! $?CBIN ) then
++        echo
++        echo 'Cannot setup ARP/wARP'
++        echo 'Variable $CBIN is not defined'
++        echo 'Please install CCP4 first'
++        goto errorsetup
++    endif
+ endif
+ if ( ! -d $CBIN ) then
+     echo
diff --git a/sci-chemistry/arp-warp-bin/metadata.xml b/sci-chemistry/arp-warp-bin/metadata.xml
new file mode 100644
index 000000000000..9ac9ffdb3a41
--- /dev/null
+++ b/sci-chemistry/arp-warp-bin/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>sci-chemistry</herd>
+</pkgmetadata>