SIMAP (Similarity Matrix of Proteins) is a public database of pre-calculated

protein similarities that plays a key role in many bioinformatics methods. It
contains about all currently published protein sequences and is continuously
updated.

The computational effort for keeping SIMAP up-to-date is constantly increasing.
Please help to update SIMAP by calculating protein similarities on your
computer.

WWW: http://boinc.bio.wzw.tum.de/boincsimap/

7 files changed, 110 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index dff99dacfa39..9dfadc1fbf3d 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -11,6 +11,7 @@
     SUBDIR += belvu
     SUBDIR += biojava
     SUBDIR += blast
+    SUBDIR += boinc-simap
     SUBDIR += clustalw
     SUBDIR += coalesce
     SUBDIR += blat
diff --git a/biology/boinc-simap/Makefile b/biology/boinc-simap/Makefile
new file mode 100644
index 000000000000..813490ac596c
--- /dev/null
+++ b/biology/boinc-simap/Makefile
@@ -0,0 +1,59 @@
+# New ports collection makefile for:	boinc-simap
+# Date created:				29 May 2006
+# Whom:					Pav Lucistnik <pav@FreeBSD.org>
+# $FreeBSD$
+#
+
+PORTNAME=	boinc-simap
+PORTVERSION=	5.08
+CATEGORIES=	biology
+MASTER_SITES=	http://boinc.bio.wzw.tum.de/boincsimap/download/
+DISTNAME=	simap_${PORTVERSION}_i386-pc-freebsd_dyn
+EXTRACT_SUFX=	#
+
+MAINTAINER=	pav@FreeBSD.org
+COMMENT=	Similarity Matrix of Proteins project for BOINC
+
+RUN_DEPENDS=	boinc_client:${PORTSDIR}/net/boinc-client
+
+NO_BUILD=	yes
+NO_WRKSUBDIR=	yes
+STRIP=		#
+
+# these must match settings in ${PORTSDIR}/net/boinc-client/Makefile
+BOINC_USER?=	boinc
+BOINC_GROUP?=	nobody
+BOINC_HOME?=	/var/db/boinc
+
+SIMAP_SITE=	boinc.bio.wzw.tum.de_boincsimap
+SIMAP_URL=	boinc.bio.wzw.tum.de/boincsimap
+SIMAP_BINARY=	${DISTNAME}
+
+PLIST_SUB=	SIMAP_BINARY=${SIMAP_BINARY} SIMAP_SITE=${SIMAP_SITE} \
+		BOINC_HOME=${BOINC_HOME}
+
+SUB_FILES=	app_info.xml
+SUB_LIST=	DISTNAME=${DISTNAME} APPVERSION=${PORTVERSION:S/.//}
+
+.include <bsd.port.pre.mk>
+
+ONLY_FOR_ARCHS=	i386 amd64
+
+.if ${OSVERSION} < 600000
+IGNORE=		only supports FreeBSD 6.X and newer
+.endif
+
+do-extract:
+	@${MKDIR} ${WRKDIR}
+	@${CP} ${DISTDIR}/${DISTNAME} ${WRKDIR}
+
+do-install:
+	${INSTALL} -d -o ${BOINC_USER} -g ${BOINC_GROUP} ${BOINC_HOME}/projects
+	${INSTALL} -d -o ${BOINC_USER} -g ${BOINC_GROUP} ${BOINC_HOME}/projects/${SIMAP_SITE}
+	${INSTALL_DATA} -o ${BOINC_USER} -g ${BOINC_GROUP} ${WRKDIR}/app_info.xml ${BOINC_HOME}/projects/${SIMAP_SITE}
+	${INSTALL_PROGRAM} -o ${BOINC_USER} -g ${BOINC_GROUP} ${WRKDIR}/${SIMAP_BINARY} ${BOINC_HOME}/projects/${SIMAP_SITE}
+
+post-install:
+	@${CAT} ${PKGMESSAGE}
+
+.include <bsd.port.post.mk>
diff --git a/biology/boinc-simap/distinfo b/biology/boinc-simap/distinfo
new file mode 100644
index 000000000000..f2b8125e5a33
--- /dev/null
+++ b/biology/boinc-simap/distinfo
@@ -0,0 +1,3 @@
+MD5 (simap_5.08_i386-pc-freebsd_dyn) = cfc33759f7132680fc3f1f6e8c03fe1a
+SHA256 (simap_5.08_i386-pc-freebsd_dyn) = 3b7bb8d150b9f41e2ff84c02b6f54008bc90448f19831cd9110e4c2981a36db2
+SIZE (simap_5.08_i386-pc-freebsd_dyn) = 950606
diff --git a/biology/boinc-simap/files/app_info.xml.in b/biology/boinc-simap/files/app_info.xml.in
new file mode 100644
index 000000000000..9e9ce6ee58ce
--- /dev/null
+++ b/biology/boinc-simap/files/app_info.xml.in
@@ -0,0 +1,17 @@
+<app_info>
+    <app>
+        <name>simap</name>
+    </app>
+    <file_info>
+        <name>%%DISTNAME%%</name>
+        <executable/>
+    </file_info>
+    <app_version>
+        <app_name>simap</app_name>
+        <version_num>%%APPVERSION%%</version_num>
+       <file_ref>
+            <file_name>%%DISTNAME%%</file_name>
+            <main_program/>
+        </file_ref>
+    </app_version>
+</app_info>
diff --git a/biology/boinc-simap/pkg-descr b/biology/boinc-simap/pkg-descr
new file mode 100644
index 000000000000..c73986116322
--- /dev/null
+++ b/biology/boinc-simap/pkg-descr
@@ -0,0 +1,10 @@
+SIMAP (Similarity Matrix of Proteins) is a public database of pre-calculated
+protein similarities that plays a key role in many bioinformatics methods. It
+contains about all currently published protein sequences and is continuously
+updated.
+
+The computational effort for keeping SIMAP up-to-date is constantly increasing.
+Please help to update SIMAP by calculating protein similarities on your
+computer.
+
+WWW: http://boinc.bio.wzw.tum.de/boincsimap/
diff --git a/biology/boinc-simap/pkg-message b/biology/boinc-simap/pkg-message
new file mode 100644
index 000000000000..cc9b9f4bf559
--- /dev/null
+++ b/biology/boinc-simap/pkg-message
@@ -0,0 +1,16 @@
+*****************************************************************************
+ATTACHING PROJECT
+
+Just run boinc_gui, choose Attach, and follow instructions.
+Project URL is boinc.bio.wzw.tum.de/boincsimap
+
+MANUAL INSTALLATION
+ *) If this is your first time in any BOINC project, create a new account at
+    http://boinc.bio.wzw.tum.de/boincsimap/create_account_form.php
+
+ *) Or get your account key at http://boinc.bio.wzw.tum.de/boincsimap/get_passwd.php
+
+ *) Attach to the project:
+    cd /var/db/boinc
+    boinc_cmd --project_attach boinc.bio.wzw.tum.de/boincsimap <account key>
+*****************************************************************************
diff --git a/biology/boinc-simap/pkg-plist b/biology/boinc-simap/pkg-plist
new file mode 100644
index 000000000000..b2721fbe82f7
--- /dev/null
+++ b/biology/boinc-simap/pkg-plist
@@ -0,0 +1,4 @@
+@cwd %%BOINC_HOME%%
+projects/%%SIMAP_SITE%%/app_info.xml
+projects/%%SIMAP_SITE%%/%%SIMAP_BINARY%%
+@unexec rmdir %D/projects/%%SIMAP_SITE%% 2>/dev/null || true