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authorMario Sergio Fujikawa Ferreira <lioux@FreeBSD.org>2002-10-07 03:07:13 +0000
committerMario Sergio Fujikawa Ferreira <lioux@FreeBSD.org>2002-10-07 03:07:13 +0000
commite6797a6f48bbdb032376b814f55246b6cd46cc29 (patch)
treea8dd9bace5168128eb98062cdd822146740d1a09 /biology/distribfold
parent70a44de6b2fcb6a6e1f91cd3cd7336962622661d (diff)
downloadports-e6797a6f48bbdb032376b814f55246b6cd46cc29.tar.gz
ports-e6797a6f48bbdb032376b814f55246b6cd46cc29.zip
Notes
Diffstat (limited to 'biology/distribfold')
-rw-r--r--biology/distribfold/Makefile116
-rw-r--r--biology/distribfold/distinfo1
-rw-r--r--biology/distribfold/files/distribfold.sh61
-rw-r--r--biology/distribfold/files/number_of_dirs.sh16
-rw-r--r--biology/distribfold/files/patch-foldit16
-rw-r--r--biology/distribfold/pkg-comment1
-rw-r--r--biology/distribfold/pkg-deinstall63
-rw-r--r--biology/distribfold/pkg-descr24
-rw-r--r--biology/distribfold/pkg-install41
-rw-r--r--biology/distribfold/pkg-message13
-rw-r--r--biology/distribfold/pkg-plist22
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