o New port distribfold version 0.1: distribfold.org distributed protein

  folding project
o One can start multiple instances of this port. Just install it
  using WITH_NCPU

11 files changed, 374 insertions, 0 deletions

diff --git a/biology/distribfold/Makefile b/biology/distribfold/Makefile
new file mode 100644
index 000000000000..a8b93ba7e881
--- /dev/null
+++ b/biology/distribfold/Makefile
@@ -0,0 +1,116 @@
+# New ports collection makefile for:	folding@home client
+# Date created:		Sun Sep 29 19:48:01 UTC 2002
+# Whom:			Mario Sergio Fujikawa Ferreira <lioux@FreeBSD.org>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	distribfold
+PORTVERSION=	0.1
+CATEGORIES=	misc net
+MASTER_SITES=	ftp://ftp.mshri.on.ca/pub/distribfold/download/
+DISTNAME=	distribfold-current-FreeBSD
+
+MAINTAINER=	lioux@FreeBSD.org
+
+ONLY_FOR_ARCHS=	i386
+USE_REINPLACE=	yes
+NO_BUILD=	yes
+
+WRKSRC=		${WRKDIR}/distribfold
+
+# files to install
+SCRIPT_FILES=	distrib-update foldit
+PROGRAM_FILES=	foldtrajlite
+# installation dir
+DESTINATION_DIR=	${PREFIX}/distribfold
+
+# default users
+DNETFOLD_USER=dnetfold
+DNETFOLD_GROUP=dnetfold
+
+# default number of processors
+WITH_NCPU?=	1
+
+post-patch:
+	@${REINPLACE_CMD} -E -e 's|%%DESTINATION_DIR%%|${DESTINATION_DIR}|' \
+		${WRKSRC}/foldit
+
+pre-install:
+# create users
+	@${SETENV} PKG_PREFIX=${PREFIX} ${SH} \
+		${PKGINSTALL} ${PKGNAME} POST-INSTALL
+
+do-install:
+# remove any patch scrap files 
+.for ext in bak orig
+	@${RM} -f ${WRKSRC}/*.${ext}
+.endfor
+# strip binaries
+.for file in ${PROGRAM_FILES}
+	@${STRIP_CMD} ${WRKSRC}/${file}
+.endfor
+# install startup script
+	@${INSTALL_SCRIPT} ${WRKDIR}/distribfold.sh ${PREFIX}/etc/rc.d
+# for every cpu directory
+	@ncpu=`${CAT} ${WRKDIR}/ncpu` ; \
+	for dir in `${FILESDIR}/number_of_dirs.sh $${ncpu}` ; do \
+		DESTINATION_DIR=${DESTINATION_DIR}/cpu$${dir} ; \
+		${MKDIR} $${DESTINATION_DIR} ; \
+		${INSTALL_DATA} ${WRKSRC}/* $${DESTINATION_DIR} ; \
+		${CHGRP} -R ${DNETFOLD_GROUP} $${DESTINATION_DIR} ; \
+		${CHMOD} g+w $${DESTINATION_DIR} ; \
+		${CHOWN} ${DNETFOLD_USER} $${DESTINATION_DIR}/* ; \
+		${CHMOD} u+w $${DESTINATION_DIR}/* ; \
+		for file in ${PROGRAM_FILES} ${SCRIPT_FILES} ; do \
+			${CHMOD} 0755 $${DESTINATION_DIR}/$${file} ; \
+		done ; \
+	done
+# display package message
+	@${CAT} ${PKGMESSAGE}
+
+post-install: cook-install-plist
+
+.include <bsd.port.pre.mk>
+
+pre-everything::
+.if ${WITH_NCPU} < 1
+	@${ECHO_MSG} "===> Number of processors HAS to be at least 1"
+	@${ECHO_MSG} "===> (${WITH_NCPU}) IS NOT"
+	@${FALSE}
+.endif
+	@${ECHO_MSG} "=======> ATTENTION <======="
+	@${ECHO_MSG} "===> If you want to have multiple copies of this program"
+	@${ECHO_MSG} "===> running in order to make better use of your SMP"
+	@${ECHO_MSG} "===> system, set WITH_CPU to the number of cpus"
+	@${ECHO_MSG} "===> available in your system"
+	@${ECHO_MSG} "===> For example, 2 cpus. \"make WITH_CPU=2\""
+	@${ECHO_MSG} "===> Do not use this variable if you do not have a SMP"
+	@${ECHO_MSG} "===> system. There is no advantage otherwise."
+
+do-configure:
+# prepare startup script
+	@${SED} -e 's|%%DNETFOLD_USER%%|${DNETFOLD_USER}|' \
+		-e 's|%%DESTINATION_DIR%%|${DESTINATION_DIR}|' \
+		-e 's|%%NCPU%%|${WITH_NCPU}|' \
+		${FILESDIR}/distribfold.sh > ${WRKDIR}/distribfold.sh
+# record number of cpus
+	@${ECHO} ${WITH_NCPU} > ${WRKDIR}/ncpu
+
+cook-install-plist: generate-plist
+.if ${WITH_NCPU} > 1
+	@${GREP} cpu0 ${TMPPLIST} > ${WRKDIR}/plist
+	@${TAIL} -n 2 ${TMPPLIST} > ${WRKDIR}/plist.end
+	@${CP} /dev/null ${WRKDIR}/plistN
+# for every cpu directory
+	@ncpu=`${CAT} ${WRKDIR}/ncpu` ; \
+	for dir in `${FILESDIR}/number_of_dirs.sh $${ncpu}` ; do \
+		${SED} -e "s|cpu0|cpu$${dir}|" ${WRKDIR}/plist >> ${WRKDIR}/plistN ; \
+	done
+	@${CP} /dev/null ${TMPPLIST}
+.for file in plistN plist.end
+	@${CAT} ${WRKDIR}/${file} >> ${TMPPLIST}
+.endfor
+.endif
+
+.include <bsd.port.post.mk>
diff --git a/biology/distribfold/distinfo b/biology/distribfold/distinfo
new file mode 100644
index 000000000000..caca45379ff2
--- /dev/null
+++ b/biology/distribfold/distinfo
@@ -0,0 +1 @@
+MD5 (distribfold-current-FreeBSD.tar.gz) = cd04da97523b2246c551198e564da3b1
diff --git a/biology/distribfold/files/distribfold.sh b/biology/distribfold/files/distribfold.sh
new file mode 100644
index 000000000000..fc6c75095c6a
--- /dev/null
+++ b/biology/distribfold/files/distribfold.sh
@@ -0,0 +1,61 @@
+#!/bin/sh
+# taken from misc/dnetc by dbaker@distributed.net
+
+prefix="%%DESTINATION_DIR%%"
+ncpu=%%NCPU%%
+
+case "$1" in
+start)
+	while [ ${ncpu} -gt 0 ];
+	do
+		# update cpu count
+		ncpu=$((${ncpu} - 1))
+
+		# dir for current cpu
+		dir="${prefix}/cpu${ncpu}"
+
+		if [ ! -d $dir ]; then
+		 logger -i "distribfold client directory doesn't exist. ($dir)."
+		 exit
+		fi
+
+		if [ ! -f $dir/foldtrajlite ]; then
+		 logger -i "distribfold client doesn't exist. ($dir/dfoldtrajlite)."
+		 exit
+		fi
+
+		if [ ! -f $dir/handle.txt ]; then
+		 logger -i "distribfold client is not configured. 'su -m %%DNETFOLD_USER%% -c $dir/foldit' to configure it."
+		 echo "distribfold client is not configured. 'su -m %%DNETFOLD_USER%% -c $dir/foldit' to configure it."
+		 exit
+		fi
+
+		# start client for current cpu
+		su -m %%DNETFOLD_USER%% -c "cd $dir && ./foldit" 2>/dev/null >/dev/null &
+	done
+
+	echo -n " distribfold"
+	;;
+stop)
+	while [ ${ncpu} -gt 0 ];
+	do
+		# update cpu count
+		ncpu=$((${ncpu} - 1))
+
+		# dir for current cpu
+		dir="${prefix}/cpu${ncpu}"
+
+		rm $dir/foldtrajlite.lock
+	done
+
+	# give clients enough time to shutdown
+	# 5 seconds minimum + 5 seconds per number of clients
+	sleep $((5 + $((5 * ${ncpu})))) && echo -n " distribfold"
+	;;
+*)
+	echo "Usage: `basename $0` {start|stop}" >&2
+	exit 64
+	;;
+esac
+
+exit 0
diff --git a/biology/distribfold/files/number_of_dirs.sh b/biology/distribfold/files/number_of_dirs.sh
new file mode 100644
index 000000000000..bdb3b87cc56b
--- /dev/null
+++ b/biology/distribfold/files/number_of_dirs.sh
@@ -0,0 +1,16 @@
+#!/bin/sh
+
+ncpu=${1}
+current_list=""
+
+while [ ${ncpu} -gt 0 ];
+do
+	# update cpu count
+	ncpu=$((${ncpu} - 1))
+
+	current_list="${current_list} ${ncpu}"
+done
+
+echo ${current_list}
+
+exit 0
diff --git a/biology/distribfold/files/patch-foldit b/biology/distribfold/files/patch-foldit
new file mode 100644
index 000000000000..3543505e05e8
--- /dev/null
+++ b/biology/distribfold/files/patch-foldit
@@ -0,0 +1,16 @@
+--- foldit.orig	Sun Sep 29 16:49:55 2002
++++ foldit	Sun Sep 29 16:50:42 2002
+@@ -1,4 +1,7 @@
+ #!/bin/sh
++
++cd %%DESTINATION_DIR%%
++
+ if [ -f donename.dat ]
+ then
+ 	rm -f tmpfoldit.bat
+@@ -23,4 +26,4 @@
+ 		fi
+ 	fi	
+ fi	
+-./foldtrajlite -f protein -n native 
++exec ./foldtrajlite -f protein -n native 
diff --git a/biology/distribfold/pkg-comment b/biology/distribfold/pkg-comment
new file mode 100644
index 000000000000..594de1538be5
--- /dev/null
+++ b/biology/distribfold/pkg-comment
@@ -0,0 +1 @@
+distribfold.org distributed protein folding project
diff --git a/biology/distribfold/pkg-deinstall b/biology/distribfold/pkg-deinstall
new file mode 100644
index 000000000000..82acb8daa0fc
--- /dev/null
+++ b/biology/distribfold/pkg-deinstall
@@ -0,0 +1,63 @@
+#! /bin/sh
+#
+# $FreeBSD: /tmp/pcvs/ports/biology/distribfold/Attic/pkg-deinstall,v 1.1 2002-10-07 03:07:13 lioux Exp $
+# taken from net/cvsup-mirror
+
+PATH=/bin:/usr/sbin
+
+DNETFOLD_USER=${DNETFOLD_USER:-dnetfold}
+DNETFOLD_GROUP=${DNETFOLD_GROUP:-dnetfold}
+
+ask() {
+    local question default answer
+
+    question=$1
+    default=$2
+    if [ -z "${PACKAGE_BUILDING}" ]; then
+	read -p "${question} [${default}]? " answer
+    fi
+    if [ x${answer} = x ]; then
+	answer=${default}
+    fi
+    echo ${answer}
+}
+
+yesno() {
+    local dflt question answer
+
+    question=$1
+    dflt=$2
+    while :; do
+	answer=$(ask "${question}" "${dflt}")
+	case "${answer}" in
+	[Yy]*)		return 0;;
+	[Nn]*)		return 1;;
+	esac
+	echo "Please answer yes or no."
+    done
+}
+
+delete_account() {
+    local u g home
+
+    u=$1
+    g=$2
+    if yesno "Do you want me to remove group \"${g}\"" y; then
+	pw groupdel -n ${g}
+	echo "Done."
+    fi
+    if yesno "Do you want me to remove user \"${u}\"" y; then
+	eval home=~${u}
+	pw userdel -n ${u}
+	echo "Done."
+	if [ -d "${home}" ]; then
+	    echo "Please remember to remove the home directory \"${home}\""
+	fi
+    fi
+}
+
+if [ x$2 != xDEINSTALL ]; then
+    exit
+fi
+
+delete_account ${DNETFOLD_USER} ${DNETFOLD_GROUP}
diff --git a/biology/distribfold/pkg-descr b/biology/distribfold/pkg-descr
new file mode 100644
index 000000000000..b43f2049ac09
--- /dev/null
+++ b/biology/distribfold/pkg-descr
@@ -0,0 +1,24 @@
+[ excerpt from developer's site ]
+
+This is the distribfold.org's client. 
+
+It makes protein structures to help sample the enormous size of
+protein conformatoinal space. We hope to find a few good samples
+and understand how a large computation can help crack the problem
+of predicting protein structure - the protein folding problem.
+
+Proteins have a vast number of folds, larger than we could hope to
+compute even with distributed computing. Usually only one fold is
+found in nature. The Distributed Folding Project aims to test our
+new protein folding algorithm. We want see if it can reproduce
+natural protein folds after making extremely large samples of many
+different folds.
+
+With your help, we will create the largest samples of protein folds
+ever computed. First we will make 1 Billion (1,000,000,000) folds
+for 5 small proteins, then we will try 10 Billion (10,000,000,000)
+for another 10 large proteins. By the end of our first phase, we
+hope to make over 100 Billion protein folds spanning 15 different
+proteins.
+
+WWW: http://www.distributedfolding.org/
diff --git a/biology/distribfold/pkg-install b/biology/distribfold/pkg-install
new file mode 100644
index 000000000000..5abebc1f8cc8
--- /dev/null
+++ b/biology/distribfold/pkg-install
@@ -0,0 +1,41 @@
+#! /bin/sh
+#
+# $FreeBSD: /tmp/pcvs/ports/biology/distribfold/Attic/pkg-install,v 1.1 2002-10-07 03:07:13 lioux Exp $
+# taken from devel/perforce
+
+PATH=/bin:/usr/sbin
+
+DNETFOLD_USER=${DNETFOLD_USER:-dnetfold}
+DNETFOLD_GROUP=${DNETFOLD_GROUP:-dnetfold}
+
+case $2 in
+POST-INSTALL)
+	USER=${DNETFOLD_USER}
+	GROUP=${DNETFOLD_GROUP}
+
+	if pw group show "${GROUP}" 2>/dev/null; then
+		echo "You already have a group \"${GROUP}\", so I will use it."
+	else
+		if pw groupadd ${GROUP} ; then
+			echo "Added group \"${GROUP}\"."
+		else
+			echo "Adding group \"${GROUP}\" failed..."
+			exit 1
+		fi
+	fi
+
+	if pw user show "${USER}" 2>/dev/null; then
+		echo "You already have a user \"${USER}\", so I will use it."
+	else
+		if pw useradd ${USER} -g ${GROUP} -h - \
+			-d /nonexistent -c "distribfold Daemon" -s /sbin/nologin
+		then
+			echo "Added user \"${USER}\"."
+		else
+			echo "Adding user \"${USER}\" failed..."
+			exit 1
+		fi
+	fi
+
+	;;
+esac
diff --git a/biology/distribfold/pkg-message b/biology/distribfold/pkg-message
new file mode 100644
index 000000000000..b80f0a4e35ca
--- /dev/null
+++ b/biology/distribfold/pkg-message
@@ -0,0 +1,13 @@
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+! REMEMBER REMEMBER REMEMBER REMEMBER REMEMBER REMEMBER REMEMBER REMEMBER !
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+You have to run '/usr/local/distribfold/cpu0/foldit' to configure it
+BEFORE trying to use distribfold.
+
+It will ask you questions on how it should work. It will NOT work
+if you do not run it and answer these questions.
+
+Do it now before you forget.
diff --git a/biology/distribfold/pkg-plist b/biology/distribfold/pkg-plist
new file mode 100644
index 000000000000..69b889f49765
--- /dev/null
+++ b/biology/distribfold/pkg-plist
@@ -0,0 +1,22 @@
+distribfold/cpu0/blpotential.txt
+distribfold/cpu0/bstdt.val
+distribfold/cpu0/cbdata
+distribfold/cpu0/CompatibilityNotes.txt
+distribfold/cpu0/copyright
+distribfold/cpu0/native.val
+distribfold/cpu0/param19_eef1.inp
+distribfold/cpu0/protein.trj
+distribfold/cpu0/readme1st.txt
+distribfold/cpu0/rotlib.bin.bz2
+distribfold/cpu0/skel.prt
+distribfold/cpu0/solvpar.inp
+distribfold/cpu0/toph19_eef1.inp
+distribfold/cpu0/whatsnew.txt
+distribfold/cpu0/zhangatm.txt
+distribfold/cpu0/zhangeij.txt
+distribfold/cpu0/distrib-update
+distribfold/cpu0/foldit
+distribfold/cpu0/foldtrajlite
+@unexec rmdir %D/distribfold/cpu0 2>/dev/null || true
+etc/rc.d/distribfold.sh
+@unexec rmdir %D/distribfold 2>/dev/null || echo "If you are permanently removing this port, you should do a ``rm -rf ${PKG_PREFIX}/distribfold`` to remove any binary, configuration and log files left." | fmt