diff options
author | Baptiste Daroussin <bapt@FreeBSD.org> | 2014-09-01 11:37:14 +0000 |
---|---|---|
committer | Baptiste Daroussin <bapt@FreeBSD.org> | 2014-09-01 11:37:14 +0000 |
commit | a76b6b5c50aa5c419d596103d4340492d94f09c3 (patch) | |
tree | 9b7b27b9d470ff8bf9122de83a9fa8e69dda28eb | |
parent | Remove *.la files (diff) |
Remove non staged ports without pending PR from b*
Notes
Notes:
svn path=/head/; revision=366862
Diffstat (limited to '')
27 files changed, 4 insertions, 2731 deletions
@@ -6527,3 +6527,7 @@ audio/festvox-us3-mbrola||2014-09-01|Not staged audio/ipod-sharp||2014-09-01|Not staged audio/linux-musicipserver||2014-09-01|Not staged audio/liquidsoap||2014-09-01|Not staged +benchmarks/spec-sfs||2014-09-01|Not staged +biology/blast||2014-09-01|Not staged +biology/embassy||2014-09-01|Not staged +biology/pymol||2014-09-01|Not staged diff --git a/benchmarks/spec-sfs/Makefile b/benchmarks/spec-sfs/Makefile deleted file mode 100644 index df577a9c6da1..000000000000 --- a/benchmarks/spec-sfs/Makefile +++ /dev/null @@ -1,63 +0,0 @@ -# Created by: Craig Rodrigues <rodrigc@FreeBSD.org> -# $FreeBSD$ -# -# Based on port originally created by Garrett Cooper <gcooper@FreeBSD.org> -# - -PORTNAME= spec-sfs -PORTVERSION= 2008 -CATEGORIES= benchmarks java -DISTNAME= SPECsfs2008-1.00 -EXTRACT_SUFX= .iso - -MAINTAINER= ports@FreeBSD.org -COMMENT= SPEC NFS and CIFS filesystem benchmark suite - -NO_PACKAGE= license restricts redistribution -RESTRICTED= license restricts redistribution - -USES= gmake perl5 -USE_PERL5= run -USE_JAVA= yes -JAVA_VERSION= 1.6+ - -SUB_FILES= pkg-message - -WRKSRC= ${WRKDIR} -BUILD_WRKSRC= ${WRKSRC}/spec-sfs2008 -DOWNLOAD_URL?= http://www.spec.org/sfs2008/ -SPEC_ROOT?= ${PREFIX}/${PORTNAME} - -DOCSDIR= ${SPEC_ROOT}/documents - -OPTIONS_DEFINE= RESERVED_PORT -OPTIONS_DEFAULT= RESERVED_PORT - -RESERVED_PORT_DESC= Use privileged ports when doing NFS testing - -RESERVED_PORT_CFLAGS= -DRESVPORT - -# Substitutions for pkg-plist -PLIST_SUB+= SPEC_ROOT=${SPEC_ROOT} - -NO_STAGE= yes -.include <bsd.port.pre.mk> - -.if !exists(${DISTDIR}/${DISTNAME}${EXTRACT_SUFX}) -IGNORE?=You must purchase ${DISTFILES} from SPEC (${DOWNLOAD_URL}), place it in ${DISTDIR} and then run make again -.endif - -pre-install: - ${FIND} ${WRKDIR} -name "*\.orig" -delete - -do-install: - cd ${WRKDIR}/spec-sfs2008/manager && ${JAVA} SpecInstall ${SPEC_ROOT} - ${RM} -fr ${SPEC_ROOT}/binaries - ${CHMOD} g+w ${SPEC_ROOT}/result - -post-install: - @${ECHO_CMD} - @${CAT} ${WRKDIR}/${PKGMESSAGE:T} - @${ECHO_CMD} - -.include <bsd.port.post.mk> diff --git a/benchmarks/spec-sfs/distinfo b/benchmarks/spec-sfs/distinfo deleted file mode 100644 index 97dadf4d45ad..000000000000 --- a/benchmarks/spec-sfs/distinfo +++ /dev/null @@ -1,2 +0,0 @@ -SHA256 (SPECsfs2008-1.00.iso) = ef7e7056c08960a2b13fff9680bbf60e5f8f3ecd0b458e1ff91a14cb198212e2 -SIZE (SPECsfs2008-1.00.iso) = 31132924 diff --git a/benchmarks/spec-sfs/files/patch-Makefile b/benchmarks/spec-sfs/files/patch-Makefile deleted file mode 100644 index 6175a953f43f..000000000000 --- a/benchmarks/spec-sfs/files/patch-Makefile +++ /dev/null @@ -1,15 +0,0 @@ ---- spec-sfs2008/Makefile.orig 2013-09-24 02:00:10.013168784 -0700 -+++ spec-sfs2008/Makefile 2013-09-24 02:02:29.965159029 -0700 -@@ -65,10 +65,10 @@ - ifeq ($(OS), freebsd) - MACHID= freebsd - CC= /usr/bin/gcc --OPT= -O -+OPT= -O0 - LIBS= -lm - OSTYPE= -DFreeBSD --EXTRA_CFLAGS= -DSETPGRP_BSD -DNO_T_TYPES -DUSE_INTTYPES $(CIFS_CFLAGS) $(MVFDN_FLAG) -+EXTRA_CFLAGS= -DSETPGRP_BSD -DNO_T_TYPES -DUSE_INTTYPES -DUSE_POSIX_SIGNALS $(CIFS_CFLAGS) $(MVFDN_FLAG) - CIFS_CFLAGS = -DCIFS_VFS_USERSPACE - RESVPORT_MOUNT= - SFSCIFS = sfscifs diff --git a/benchmarks/spec-sfs/files/patch-libcifs-connect.c b/benchmarks/spec-sfs/files/patch-libcifs-connect.c deleted file mode 100644 index 6ddb8ef5cc49..000000000000 --- a/benchmarks/spec-sfs/files/patch-libcifs-connect.c +++ /dev/null @@ -1,26 +0,0 @@ ---- spec-sfs2008/redistributable_sources/libcifs/connect.c.orig 2008-02-02 21:30:04.000000000 -0800 -+++ spec-sfs2008/redistributable_sources/libcifs/connect.c 2011-08-20 15:50:55.000000000 -0700 -@@ -19,6 +19,9 @@ - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA - */ - -+#if defined(FreeBSD) -+#include <sys/param.h> -+#endif - #ifndef CIFS_VFS_USERSPACE - #include <linux/fs.h> - #include <linux/net.h> -@@ -102,9 +105,10 @@ - unsigned short int port; - }; - --#if defined(FreeBSD) || defined(SOLARIS2) || defined(macosx) --int --strnlen(char *a,int len) -+#if (defined(FreeBSD) && __FreeBSD_version < 800067) || \ -+ defined(SOLARIS2) || defined(macosx) -+size_t -+strnlen(const char *a, size_t maxlen) - { - int i,j; - j=0; diff --git a/benchmarks/spec-sfs/files/patch-post_install.sh b/benchmarks/spec-sfs/files/patch-post_install.sh deleted file mode 100644 index dd6100f537b8..000000000000 --- a/benchmarks/spec-sfs/files/patch-post_install.sh +++ /dev/null @@ -1,11 +0,0 @@ ---- spec-sfs2008/post_install.sh.orig 2013-09-23 14:24:56.000000000 -0700 -+++ spec-sfs2008/post_install.sh 2013-09-23 14:25:16.000000000 -0700 -@@ -19,7 +19,7 @@ - # - # Fix up the binaries - # --for i in binaries/* -+for i in binaries/* bin - do - if [ -f $i/sfsnfs3 ]; then - chmod 755 $i/sfs* diff --git a/benchmarks/spec-sfs/files/patch-src-Makefile b/benchmarks/spec-sfs/files/patch-src-Makefile deleted file mode 100644 index bf723b76fb4f..000000000000 --- a/benchmarks/spec-sfs/files/patch-src-Makefile +++ /dev/null @@ -1,11 +0,0 @@ ---- spec-sfs2008/src/Makefile.orig 2013-09-12 16:56:55.851060286 -0700 -+++ spec-sfs2008/src/Makefile 2013-09-12 16:57:25.012057145 -0700 -@@ -216,7 +216,7 @@ - - ${RPCLIB}: FRC - @cd rpc; ${MAKE} MACHID="${MACHID}" \ -- CC="${CC}" CFLAGS="${CFLAGS}" \ -+ CC="${CC}" CFLAGS="${CFLAGS}" DEBUG="${DEBUG}" \ - LDFLAGS="${LDFLAGS}" EXTRA_CFLAGS="${EXTRA_CFLAGS}" \ - EXTRA_LDFLAGS="${EXTRA_LDFLAGS}" EXTRA_LIBS="${EXTRA_LIBS}" \ - LIBS="${LIBS}" OSTYPE="${OSTYPE}" OPT="${OPT}" \ diff --git a/benchmarks/spec-sfs/files/patch-submit_tools-Makefile b/benchmarks/spec-sfs/files/patch-submit_tools-Makefile deleted file mode 100644 index 259a54a76f75..000000000000 --- a/benchmarks/spec-sfs/files/patch-submit_tools-Makefile +++ /dev/null @@ -1,19 +0,0 @@ ---- spec-sfs2008/submit_tools/Makefile.orig 2013-09-12 13:38:44.941878849 -0700 -+++ spec-sfs2008/submit_tools/Makefile 2013-09-12 13:39:15.160876702 -0700 -@@ -10,12 +10,12 @@ - INSTALLDIR=. - - install: -- cd $(SPECREPORT); make install -- cd $(SUBEDIT); make install -+ cd $(SPECREPORT); $(MAKE) install -+ cd $(SUBEDIT); $(MAKE) install - - clean: -- cd $(SPECREPORT); make clean -- cd $(SUBEDIT); make clean -+ cd $(SPECREPORT); $(MAKE) clean -+ cd $(SUBEDIT); $(MAKE) clean - - uninstall: - cd $(INSTALLDIR); rm -f specreport.pl subedit.pl diff --git a/benchmarks/spec-sfs/files/pkg-message.in b/benchmarks/spec-sfs/files/pkg-message.in deleted file mode 100644 index 6db58cefaf88..000000000000 --- a/benchmarks/spec-sfs/files/pkg-message.in +++ /dev/null @@ -1,3 +0,0 @@ -Be sure to read through the documentation in -%%DOCSDIR%% for how to properly -setup SPECsfs2008. diff --git a/benchmarks/spec-sfs/pkg-descr b/benchmarks/spec-sfs/pkg-descr deleted file mode 100644 index a76a31236d65..000000000000 --- a/benchmarks/spec-sfs/pkg-descr +++ /dev/null @@ -1,16 +0,0 @@ -SPECsfs2008: the SPEC NFSv3/CIFS benchmark - -SPECsfs2008 is the latest version of the Standard Performance Evaluation -Corporation benchmark suite measuring file server throughput and response time, -providing a standardized method for comparing performance across different -vendor platforms. SPECsfs2008 results summarize the server's capabilities with -respect to the number of operations that can be handled per second, as well as -the overall latency of the operations. The suite is a follow-on to the SFS97_R1 -benchmark, adding a CIFS workload, an updated NFSv3 workload, support for -additional client platforms, and a new test harness and reporting/submission -framework. - -The ISO for SPECsfs2008 must be purchased from SPEC's web site, before -this port can be built. - -WWW: http://www.spec.org/sfs2008/ diff --git a/benchmarks/spec-sfs/pkg-message b/benchmarks/spec-sfs/pkg-message deleted file mode 100644 index b14df6442ea5..000000000000 --- a/benchmarks/spec-sfs/pkg-message +++ /dev/null @@ -1 +0,0 @@ -Hi diff --git a/benchmarks/spec-sfs/pkg-plist b/benchmarks/spec-sfs/pkg-plist deleted file mode 100644 index b4172031b05b..000000000000 --- a/benchmarks/spec-sfs/pkg-plist +++ /dev/null @@ -1,591 +0,0 @@ -%%SPEC_ROOT%%/bin/sfsnfs3 -%%SPEC_ROOT%%/bin/sfs_syncd -%%SPEC_ROOT%%/bin/sfs_ext_mon -%%SPEC_ROOT%%/bin/sfs_prime -%%SPEC_ROOT%%/bin/sfscifs -%%SPEC_ROOT%%/bin/.empty -%%SPEC_ROOT%%/src/sfs_c_dmp.c -%%SPEC_ROOT%%/src/sfs_m_prm.o -%%SPEC_ROOT%%/src/sfs_c_def.h -%%SPEC_ROOT%%/src/sfs_ext_mon -%%SPEC_ROOT%%/src/sfs_c_pnt.o -%%SPEC_ROOT%%/src/rpc/svc_auth.h -%%SPEC_ROOT%%/src/rpc/pmap_clnt.o -%%SPEC_ROOT%%/src/rpc/auth.h -%%SPEC_ROOT%%/src/rpc/xdr_array.c -%%SPEC_ROOT%%/src/rpc/clnt_tcp.o -%%SPEC_ROOT%%/src/rpc/rpcb_getport.c -%%SPEC_ROOT%%/src/rpc/librpclib.a -%%SPEC_ROOT%%/src/rpc/get_myaddress.c -%%SPEC_ROOT%%/src/rpc/rpc_msg.h -%%SPEC_ROOT%%/src/rpc/clnt_udp.o -%%SPEC_ROOT%%/src/rpc/sfs_cudp.c -%%SPEC_ROOT%%/src/rpc/osdep.h -%%SPEC_ROOT%%/src/rpc/svc_tcp.c -%%SPEC_ROOT%%/src/rpc/xdr_mem.c -%%SPEC_ROOT%%/src/rpc/svc_udp.c -%%SPEC_ROOT%%/src/rpc/rpc_commondata.o -%%SPEC_ROOT%%/src/rpc/sfs_ctcp.c -%%SPEC_ROOT%%/src/rpc/xdr_float.o -%%SPEC_ROOT%%/src/rpc/svc_simple.o -%%SPEC_ROOT%%/src/rpc/svc_auth_unix.o -%%SPEC_ROOT%%/src/rpc/clnt_simple.o -%%SPEC_ROOT%%/src/rpc/xdr_rec.c -%%SPEC_ROOT%%/src/rpc/svc_auth.o -%%SPEC_ROOT%%/src/rpc/pmap_getport.c -%%SPEC_ROOT%%/src/rpc/pmap_clnt.h -%%SPEC_ROOT%%/src/rpc/svc_run.c -%%SPEC_ROOT%%/src/rpc/xdr_reference.o -%%SPEC_ROOT%%/src/rpc/xdr.c -%%SPEC_ROOT%%/src/rpc/auth_unix.o -%%SPEC_ROOT%%/src/rpc/xdr_stdio.c -%%SPEC_ROOT%%/src/rpc/pmap_rmt.h -%%SPEC_ROOT%%/src/rpc/pmap_prot.o -%%SPEC_ROOT%%/src/rpc/clnt_generic.c -%%SPEC_ROOT%%/src/rpc/rpc_prot.o -%%SPEC_ROOT%%/src/rpc/authunix_prot.o -%%SPEC_ROOT%%/src/rpc/bindresvport.o -%%SPEC_ROOT%%/src/rpc/pmap_prot2.c -%%SPEC_ROOT%%/src/rpc/svc.c -%%SPEC_ROOT%%/src/rpc/auth_none.c -%%SPEC_ROOT%%/src/rpc/pmap_prot.h -%%SPEC_ROOT%%/src/rpc/auth_unix.h -%%SPEC_ROOT%%/src/rpc/clnt_perror.c -%%SPEC_ROOT%%/src/rpc/svc_raw.o -%%SPEC_ROOT%%/src/rpc/rpc_callmsg.o -%%SPEC_ROOT%%/src/rpc/rpc_dtablesize.o -%%SPEC_ROOT%%/src/rpc/getrpcport.c -%%SPEC_ROOT%%/src/rpc/xdr_array.o -%%SPEC_ROOT%%/src/rpc/getrpcent.c -%%SPEC_ROOT%%/src/rpc/pmap_clnt.c -%%SPEC_ROOT%%/src/rpc/clnt_udp.c -%%SPEC_ROOT%%/src/rpc/get_myaddress.o -%%SPEC_ROOT%%/src/rpc/rpcb_clnt.h -%%SPEC_ROOT%%/src/rpc/netdb.h -%%SPEC_ROOT%%/src/rpc/clnt_tcp.c -%%SPEC_ROOT%%/src/rpc/rpcb_getport.o -%%SPEC_ROOT%%/src/rpc/rpc_commondata.c -%%SPEC_ROOT%%/src/rpc/sfs_ctcp.o -%%SPEC_ROOT%%/src/rpc/xdr_float.c -%%SPEC_ROOT%%/src/rpc/xdr_mem.o -%%SPEC_ROOT%%/src/rpc/svc_udp.o -%%SPEC_ROOT%%/src/rpc/svc_tcp.o -%%SPEC_ROOT%%/src/rpc/sfs_cudp.o -%%SPEC_ROOT%%/src/rpc/xdr_rec.o -%%SPEC_ROOT%%/src/rpc/clnt.h -%%SPEC_ROOT%%/src/rpc/svc_auth.c -%%SPEC_ROOT%%/src/rpc/pmap_getport.o -%%SPEC_ROOT%%/src/rpc/types.h -%%SPEC_ROOT%%/src/rpc/pmap_getmaps.c -%%SPEC_ROOT%%/src/rpc/svc_simple.c -%%SPEC_ROOT%%/src/rpc/svc_auth_unix.c -%%SPEC_ROOT%%/src/rpc/clnt_simple.c -%%SPEC_ROOT%%/src/rpc/pmap_prot.c -%%SPEC_ROOT%%/src/rpc/auth_unix.c -%%SPEC_ROOT%%/src/rpc/xdr_stdio.o -%%SPEC_ROOT%%/src/rpc/rpc.h -%%SPEC_ROOT%%/src/rpc/xdr.o -%%SPEC_ROOT%%/src/rpc/xdr_reference.c -%%SPEC_ROOT%%/src/rpc/svc_run.o -%%SPEC_ROOT%%/src/rpc/bindresvport.c -%%SPEC_ROOT%%/src/rpc/authunix_prot.c -%%SPEC_ROOT%%/src/rpc/rpcb_prot.h -%%SPEC_ROOT%%/src/rpc/rpc_prot.c -%%SPEC_ROOT%%/src/rpc/svc.h -%%SPEC_ROOT%%/src/rpc/auth_none.o -%%SPEC_ROOT%%/src/rpc/pmap_prot2.o -%%SPEC_ROOT%%/src/rpc/svc.o -%%SPEC_ROOT%%/src/rpc/Makefile -%%SPEC_ROOT%%/src/rpc/rpc_dtablesize.c -%%SPEC_ROOT%%/src/rpc/socket_gen.h -%%SPEC_ROOT%%/src/rpc/xdr.h -%%SPEC_ROOT%%/src/rpc/rpc_callmsg.c -%%SPEC_ROOT%%/src/rpc/clnt_perror.o -%%SPEC_ROOT%%/src/rpc/svc_raw.c -%%SPEC_ROOT%%/src/rpc/pmap_rmt.c -%%SPEC_ROOT%%/src/sfs_cifs_ops.c -%%SPEC_ROOT%%/src/sfs_c_man.o -%%SPEC_ROOT%%/src/sfs_c_bio.c -%%SPEC_ROOT%%/src/sfs_c_sub.o -%%SPEC_ROOT%%/src/sfs_c_clnt.o -%%SPEC_ROOT%%/src/sfs_c_sig.o -%%SPEC_ROOT%%/src/sfs_cifs_vld.c -%%SPEC_ROOT%%/src/sfs_m_def.h -%%SPEC_ROOT%%/src/sfs_c_chd.c -%%SPEC_ROOT%%/src/sfs_c_hmm.o -%%SPEC_ROOT%%/src/sfs_m_msg.o -%%SPEC_ROOT%%/src/sfs_c_chd_cifs.c -%%SPEC_ROOT%%/src/sfs_3_xdr.o -%%SPEC_ROOT%%/src/sfs_m_snc.c -%%SPEC_ROOT%%/src/sfs_m_xdr.o -%%SPEC_ROOT%%/src/sfs_c_hsh.h -%%SPEC_ROOT%%/src/sfs_c_cifs.c -%%SPEC_ROOT%%/src/sfs_c_mnt.o -%%SPEC_ROOT%%/src/sfs_suchown -%%SPEC_ROOT%%/src/sfs_c_dat.c -%%SPEC_ROOT%%/src/sfs_c_nfs.c -%%SPEC_ROOT%%/src/sfs_c_clk.o -%%SPEC_ROOT%%/src/sfs_c_hsh.o -%%SPEC_ROOT%%/src/sfs_3_vld.c -%%SPEC_ROOT%%/src/sfs_3_ops.c -%%SPEC_ROOT%%/src/sfs_c_rnd.o -%%SPEC_ROOT%%/src/sfs_c_mnt_cifs.c -%%SPEC_ROOT%%/src/sfs_m_prm.c -%%SPEC_ROOT%%/src/sfs_c_dmp.o -%%SPEC_ROOT%%/src/UnivSystem.sh -%%SPEC_ROOT%%/src/sfs_c_pnt.c -%%SPEC_ROOT%%/src/Makefile -%%SPEC_ROOT%%/src/sfs_c_bio.o -%%SPEC_ROOT%%/src/sfs_c_sub.c -%%SPEC_ROOT%%/src/sfs_sync.x -%%SPEC_ROOT%%/src/sfs_cifs_ops.o -%%SPEC_ROOT%%/src/sfs_c_man.c -%%SPEC_ROOT%%/src/sfs_c_sig.c -%%SPEC_ROOT%%/src/sfs_c_types.h -%%SPEC_ROOT%%/src/sfs_cifs_vld.o -%%SPEC_ROOT%%/src/sfs_c_clnt.c -%%SPEC_ROOT%%/src/sfs_c_chd_cifs.o -%%SPEC_ROOT%%/src/sfs_m_msg.c -%%SPEC_ROOT%%/src/sfs_c_chd.o -%%SPEC_ROOT%%/src/sfs_c_hmm.c -%%SPEC_ROOT%%/src/sfs_c_mnt.c -%%SPEC_ROOT%%/src/sfs_c_nfs.h -%%SPEC_ROOT%%/src/sfs_c_cifs.o -%%SPEC_ROOT%%/src/sfs_3_xdr.c -%%SPEC_ROOT%%/src/sfs_m_snc.o -%%SPEC_ROOT%%/src/sfs_m_xdr.c -%%SPEC_ROOT%%/src/sfs_c_clk.c -%%SPEC_ROOT%%/src/sfs_c_hsh.c -%%SPEC_ROOT%%/src/sfs_c_cifs.h -%%SPEC_ROOT%%/src/sfs_3_vld.o -%%SPEC_ROOT%%/src/sfs_ext_mon.bat -%%SPEC_ROOT%%/src/sfs_c_dat.o -%%SPEC_ROOT%%/src/sfs_c_nfs.o -%%SPEC_ROOT%%/src/sfs_c_mnt_cifs.o -%%SPEC_ROOT%%/src/win32/win32_signum.h -%%SPEC_ROOT%%/src/win32/win32_stdint.h -%%SPEC_ROOT%%/src/win32/win32_getopt.c -%%SPEC_ROOT%%/src/win32/win32_if.h -%%SPEC_ROOT%%/src/win32/win32_sub.h -%%SPEC_ROOT%%/src/win32/win32_errno.h -%%SPEC_ROOT%%/src/win32/win32_types.h -%%SPEC_ROOT%%/src/win32/win32_getopt.h -%%SPEC_ROOT%%/src/win32/win32_portmap.c -%%SPEC_ROOT%%/src/win32/VS2005/win32_portmap/win32_portmap.vcproj -%%SPEC_ROOT%%/src/win32/VS2005/sfs_prime/sfs_prime.vcproj -%%SPEC_ROOT%%/src/win32/VS2005/sfs_syncd/sfs_syncd.vcproj -%%SPEC_ROOT%%/src/win32/VS2005/sfscifs/sfscifs.vcproj -%%SPEC_ROOT%%/src/win32/VS2005/SFS_WIN32.sln -%%SPEC_ROOT%%/src/win32/VS2005/cleanup.bat -%%SPEC_ROOT%%/src/win32/VS2005/rpc/rpc.vcproj -%%SPEC_ROOT%%/src/win32/VS2005/sfsnfs3/sfsnfs3.vcproj -%%SPEC_ROOT%%/src/win32/VS2005/libcifs/libcifs.vcproj -%%SPEC_ROOT%%/src/win32/win32_sub.c -%%SPEC_ROOT%%/src/sfs_c_rnd.c -%%SPEC_ROOT%%/src/sfs_3_ops.o -%%SPEC_ROOT%%/post_install.sh -%%SPEC_ROOT%%/documents/pdf/SPECsfs2008_run_rules.pdf -%%SPEC_ROOT%%/documents/pdf/SPECsfs2008_users_guide.pdf -%%SPEC_ROOT%%/documents/pdf/.empty -%%SPEC_ROOT%%/documents/html/SPECsfs2008_users_guide.htm -%%SPEC_ROOT%%/documents/html/SPECsfs2008_run_rules_files/image003.wmz -%%SPEC_ROOT%%/documents/html/SPECsfs2008_run_rules_files/filelist.xml -%%SPEC_ROOT%%/documents/html/SPECsfs2008_run_rules_files/image006.gif -%%SPEC_ROOT%%/documents/html/SPECsfs2008_run_rules_files/image005.wmz -%%SPEC_ROOT%%/documents/html/SPECsfs2008_run_rules_files/header.htm -%%SPEC_ROOT%%/documents/html/SPECsfs2008_run_rules_files/image002.gif -%%SPEC_ROOT%%/documents/html/SPECsfs2008_run_rules_files/image001.wmz -%%SPEC_ROOT%%/documents/html/SPECsfs2008_run_rules_files/image004.gif -%%SPEC_ROOT%%/documents/html/SPECsfs2008_run_rules.htm -%%SPEC_ROOT%%/documents/html/.empty -%%SPEC_ROOT%%/documents/html/SPECsfs2008_users_guide_files/filelist.xml -%%SPEC_ROOT%%/documents/html/SPECsfs2008_users_guide_files/image007.gif -%%SPEC_ROOT%%/documents/html/SPECsfs2008_users_guide_files/header.htm -%%SPEC_ROOT%%/documents/html/SPECsfs2008_users_guide_files/image001.gif -%%SPEC_ROOT%%/documents/html/SPECsfs2008_users_guide_files/image006.gif -%%SPEC_ROOT%%/documents/html/SPECsfs2008_users_guide_files/image005.gif -%%SPEC_ROOT%%/documents/html/SPECsfs2008_users_guide_files/image002.gif -%%SPEC_ROOT%%/documents/html/SPECsfs2008_users_guide_files/image003.gif -%%SPEC_ROOT%%/documents/html/SPECsfs2008_users_guide_files/image004.gif -%%SPEC_ROOT%%/documents/ms-word/SPECsfs2008_run_rules.doc -%%SPEC_ROOT%%/documents/ms-word/SPECsfs2008_users_guide.doc -%%SPEC_ROOT%%/redistributable_sources/XML-XPath-1.13.tar.gz -%%SPEC_ROOT%%/redistributable_sources/jcommon-1.0.8.tar.gz -%%SPEC_ROOT%%/redistributable_sources/XML-Parser_license.txt -%%SPEC_ROOT%%/redistributable_sources/libcifs/misc.o -%%SPEC_ROOT%%/redistributable_sources/libcifs/cifspdu.h -%%SPEC_ROOT%%/redistributable_sources/libcifs/md4.c -%%SPEC_ROOT%%/redistributable_sources/libcifs/bsd_smbdes.o -%%SPEC_ROOT%%/redistributable_sources/libcifs/interface.h -%%SPEC_ROOT%%/redistributable_sources/libcifs/status_code.c -%%SPEC_ROOT%%/redistributable_sources/libcifs/test_smbdes.c -%%SPEC_ROOT%%/redistributable_sources/libcifs/testconnect -%%SPEC_ROOT%%/redistributable_sources/libcifs/x86_linux.h -%%SPEC_ROOT%%/redistributable_sources/libcifs/des_locl.h -%%SPEC_ROOT%%/redistributable_sources/libcifs/connect.c -%%SPEC_ROOT%%/redistributable_sources/libcifs/sk.h -%%SPEC_ROOT%%/redistributable_sources/libcifs/libcifs.a 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%%SPEC_ROOT%%/submit_tools/subedit -@dirrm %%SPEC_ROOT%%/submit_tools/specreport/lib -@dirrm %%SPEC_ROOT%%/submit_tools/specreport/XML/t -@dirrm %%SPEC_ROOT%%/submit_tools/specreport/XML/examples -@dirrm %%SPEC_ROOT%%/submit_tools/specreport/XML/XPath/Node -@dirrm %%SPEC_ROOT%%/submit_tools/specreport/XML/XPath -@dirrm %%SPEC_ROOT%%/submit_tools/specreport/XML -@dirrm %%SPEC_ROOT%%/submit_tools/specreport -@dirrm %%SPEC_ROOT%%/submit_tools/lib/XML/t -@dirrm %%SPEC_ROOT%%/submit_tools/lib/XML/examples -@dirrm %%SPEC_ROOT%%/submit_tools/lib/XML/XPath/Node -@dirrm %%SPEC_ROOT%%/submit_tools/lib/XML/XPath -@dirrm %%SPEC_ROOT%%/submit_tools/lib/XML -@dirrm %%SPEC_ROOT%%/submit_tools/lib -@dirrm %%SPEC_ROOT%%/submit_tools/examples -@dirrm %%SPEC_ROOT%%/submit_tools/dev -@dirrm %%SPEC_ROOT%%/submit_tools -@dirrm %%SPEC_ROOT%%/src/win32/VS2005/win32_portmap -@dirrm %%SPEC_ROOT%%/src/win32/VS2005/sfsnfs3 -@dirrm %%SPEC_ROOT%%/src/win32/VS2005/sfscifs -@dirrm %%SPEC_ROOT%%/src/win32/VS2005/sfs_syncd -@dirrm %%SPEC_ROOT%%/src/win32/VS2005/sfs_prime -@dirrm %%SPEC_ROOT%%/src/win32/VS2005/rpc -@dirrm %%SPEC_ROOT%%/src/win32/VS2005/libcifs -@dirrm %%SPEC_ROOT%%/src/win32/VS2005 -@dirrm %%SPEC_ROOT%%/src/win32 -@dirrm %%SPEC_ROOT%%/src/rpc -@dirrm %%SPEC_ROOT%%/src -@dirrm %%SPEC_ROOT%%/result -@dirrm %%SPEC_ROOT%%/redistributable_sources/libcifs -@dirrm %%SPEC_ROOT%%/redistributable_sources -@dirrm %%SPEC_ROOT%%/manager/javacc-3.2/doc -@dirrm %%SPEC_ROOT%%/manager/javacc-3.2/bin/lib -@dirrm %%SPEC_ROOT%%/manager/javacc-3.2/bin -@dirrm %%SPEC_ROOT%%/manager/javacc-3.2 -@dirrm %%SPEC_ROOT%%/manager -@dirrm %%SPEC_ROOT%%/documents/pdf -@dirrm %%SPEC_ROOT%%/documents/ms-word -@dirrm %%SPEC_ROOT%%/documents/html/SPECsfs2008_users_guide_files -@dirrm %%SPEC_ROOT%%/documents/html/SPECsfs2008_run_rules_files -@dirrm %%SPEC_ROOT%%/documents/html -@dirrm %%SPEC_ROOT%%/documents -@dirrm %%SPEC_ROOT%%/bin -@dirrm %%SPEC_ROOT%% diff --git a/biology/Makefile b/biology/Makefile index 458c72813d4e..14f7b8a61350 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -9,14 +9,12 @@ SUBDIR += babel SUBDIR += biococoa SUBDIR += biojava - SUBDIR += blast SUBDIR += blat SUBDIR += boinc-simap SUBDIR += chemeq SUBDIR += clustalw SUBDIR += consed SUBDIR += crux - SUBDIR += embassy SUBDIR += emboss SUBDIR += fasta SUBDIR += fasta3 @@ -74,7 +72,6 @@ SUBDIR += py-biopython SUBDIR += pycogent SUBDIR += pyfasta - SUBDIR += pymol SUBDIR += python-nexus SUBDIR += recombine SUBDIR += ruby-bio diff --git a/biology/blast/Makefile b/biology/blast/Makefile deleted file mode 100644 index 30fc47cd1ca3..000000000000 --- a/biology/blast/Makefile +++ /dev/null @@ -1,77 +0,0 @@ -# Created by: Fernan Aguero <fernan@iib.unsam.edu.ar> -# $FreeBSD$ - -PORTNAME= wu-blast -PORTVERSION= 2.0 -PORTREVISION= 20060322 # YYYYMMDD -CATEGORIES= biology -MASTER_SITES= # -EXTRACT_SUFX= .tar.Z - -MAINTAINER= ports@FreeBSD.org -COMMENT= WU BLAST, a software package for sequence similarity searches - -BROKEN= Mark as broken: no checksum provided - -DEPRECATED= Rights to BLAST 2.0 (WU-BLAST) have been acquired by Advanced Biocomputing, LLC -EXPIRATION_DATE=2014-09-04 - -RESTRICTED= License does not allow redistribution of binaries. You should first register for the software, which is free for academic use. -ONLY_FOR_ARCHS= i386 amd64 - -NO_BUILD= yes -DOWNLOAD_URL= http://blast.wustl.edu/licensing - -NO_WRKSUBDIR= yes - -PORTDOCS= COPYRIGHT FAQ-Indexing.html HISTORY LICENSE Memory.html \ - README.html parameters.html tabular.html -BINS= blasta gb2fasta gt2fasta memfile nrdb pam patdb \ - pir2fasta sp2fasta xdformat xdget -SCRIPTS= wu-blastall wu-formatdb -BLASTA_LINKS= blastn blastp blastx tblastn tblastx -XDFORMAT_LINKS= setdb pressdb -SUB_FILES= pkg-message - -NO_STAGE= yes -.include <bsd.port.pre.mk> - -.if ${ARCH} == amd64 -DISTNAME= blast${PORTVERSION:S/.0//}.freebsd-6.x-x64 -.else -DISTNAME= blast${PORTVERSION:S/.0//}.freebsd-6.x-i686 -.endif - -.if !exists(${DISTDIR}/${DISTNAME}${EXTRACT_SUFX}) -IGNORE= You must manually fetch ${PORTNAME}${PORTVERSION:S/.0//} for the FreeBSD platform (${DISTNAME}${EXTRACT_SUFX}) from ${DOWNLOAD_URL}, place it in ${DISTDIR} and then run make again -.endif - -do-install: -.for bin in ${BINS} - ${INSTALL_PROGRAM} ${WRKSRC}/${bin} ${PREFIX}/bin -.endfor -.for script in ${SCRIPTS} - ${INSTALL_SCRIPT} ${WRKSRC}/${script} ${PREFIX}/bin -.endfor - ${CHMOD} a-rw,a+x ${PREFIX}/bin/blasta -.for blink in ${BLASTA_LINKS} - @(cd ${PREFIX}/bin && ${LN} -s blasta ${blink}) -.endfor -.for xlink in ${XDFORMAT_LINKS} - @(cd ${PREFIX}/bin && ${LN} -s xdformat ${xlink}) -.endfor -.if ${PORT_OPTIONS:MDOCS} - @${MKDIR} ${DOCSDIR} -.for doc in ${PORTDOCS} - ${INSTALL_MAN} ${WRKSRC}/${doc} ${DOCSDIR} -.endfor -.endif - ${MKDIR} ${DATADIR} - ${CP} -R ${WRKSRC}/matrix ${DATADIR} - ${CP} -R ${WRKSRC}/filter ${DATADIR} - ${CP} ${WRKSRC}/sysblast.sample ${DATADIR} - -post-install: - @${CAT} ${PKGMESSAGE} - -.include <bsd.port.post.mk> diff --git a/biology/blast/distinfo b/biology/blast/distinfo deleted file mode 100644 index 6d040eaf212e..000000000000 --- a/biology/blast/distinfo +++ /dev/null @@ -1,2 +0,0 @@ -SHA256 (blast2.freebsd-6.x-i686.tar.Z) = IGNORE -SHA256 (blast2.freebsd-6.x-x64.tar.Z) = IGNORE diff --git a/biology/blast/files/pkg-message.in b/biology/blast/files/pkg-message.in deleted file mode 100644 index c2fa0c29be37..000000000000 --- a/biology/blast/files/pkg-message.in +++ /dev/null @@ -1,15 +0,0 @@ -====================================================================== - -A sample configuration file has been installed in %%DATADIR%% and named -sysblast.sample. Edit it to suit your needs, rename it to 'sysblast' and -place it under /etc so that it can be recognized at runtime by the blast -executable. - -Matrix files and filter executables have been placed in -%%DATADIR%%/matrix and %%DATADIR%%/filter, respectively. -You should set environment variables WUBLASTMAT and WUBLASTFILTER -(pointing to the respective directories) so that the blast executable -can find them. - -====================================================================== - diff --git a/biology/blast/pkg-descr b/biology/blast/pkg-descr deleted file mode 100644 index 902e6fbcb5be..000000000000 --- a/biology/blast/pkg-descr +++ /dev/null @@ -1,18 +0,0 @@ -Washington University BLAST (WU BLAST) version 2.0 is a powerful -software package for gene and protein identification, using sensitive, -selective and rapid similarity searches of protein and nucleotide -sequence databases. WU BLAST 2.0 builds upon WU BLAST 1.4, which in turn -was based on the public domain NCBI BLAST version 1.4. While NCBI BLAST -and WU BLAST 1.4 are in the public domain, WU BLAST 2.0 contains -significant new features and extended capabilities, the development of -which began in late 1994, at Washington University in Saint Louis. First -released in May 1996, or more than a year ahead of the NCBI, WU BLAST -2.0 is the original gapped BLAST with statistics and is known for -setting higher standards for sensitivity, speed, correctness and -accuracy, scalability and reliability than competing programs and -implementations. WU BLAST is neither a re-hashed nor "Mac-ified" version -of NCBI BLAST, although WU BLAST in many ways is easier to use. WU BLAST -essentially shares no code with NCBI BLAST, except for portions that -both packages derived from ungapped NCBI BLAST 1.4. - -WWW: http://blast.wustl.edu diff --git a/biology/blast/pkg-plist b/biology/blast/pkg-plist deleted file mode 100644 index 0933560e1e2e..000000000000 --- a/biology/blast/pkg-plist +++ /dev/null @@ -1,219 +0,0 @@ -bin/blasta -bin/gb2fasta -bin/gt2fasta -bin/memfile -bin/nrdb -bin/pam -bin/patdb -bin/pir2fasta -bin/sp2fasta -bin/xdformat -bin/xdget -bin/wu-blastall -bin/wu-formatdb -bin/blastn -bin/blastp -bin/blastx -bin/tblastn -bin/tblastx -bin/setdb -bin/pressdb -%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT -%%PORTDOCS%%%%DOCSDIR%%/FAQ-Indexing.html -%%PORTDOCS%%%%DOCSDIR%%/HISTORY -%%PORTDOCS%%%%DOCSDIR%%/LICENSE -%%PORTDOCS%%%%DOCSDIR%%/Memory.html -%%PORTDOCS%%%%DOCSDIR%%/README.html -%%PORTDOCS%%%%DOCSDIR%%/parameters.html -%%PORTDOCS%%%%DOCSDIR%%/parameters.pdf -%%PORTDOCS%%%%DOCSDIR%%/tabular.html -%%DATADIR%%/matrix/aa/nuc.4.4 -%%DATADIR%%/matrix/aa/BLOSUM30 -%%DATADIR%%/matrix/aa/BLOSUM35 -%%DATADIR%%/matrix/aa/BLOSUM40 -%%DATADIR%%/matrix/aa/BLOSUM45 -%%DATADIR%%/matrix/aa/BLOSUM50 -%%DATADIR%%/matrix/aa/BLOSUM55 -%%DATADIR%%/matrix/aa/BLOSUM60 -%%DATADIR%%/matrix/aa/BLOSUM62 -%%DATADIR%%/matrix/aa/BLOSUM65 -%%DATADIR%%/matrix/aa/BLOSUM70 -%%DATADIR%%/matrix/aa/BLOSUM75 -%%DATADIR%%/matrix/aa/BLOSUM80 -%%DATADIR%%/matrix/aa/BLOSUM85 -%%DATADIR%%/matrix/aa/BLOSUM90 -%%DATADIR%%/matrix/aa/BLOSUMN -%%DATADIR%%/matrix/aa/blosum100 -%%DATADIR%%/matrix/aa/blosum30 -%%DATADIR%%/matrix/aa/blosum35 -%%DATADIR%%/matrix/aa/blosum40 -%%DATADIR%%/matrix/aa/blosum45 -%%DATADIR%%/matrix/aa/blosum50 -%%DATADIR%%/matrix/aa/blosum55 -%%DATADIR%%/matrix/aa/blosum60 -%%DATADIR%%/matrix/aa/blosumn -%%DATADIR%%/matrix/aa/blosum62 -%%DATADIR%%/matrix/aa/blosum65 -%%DATADIR%%/matrix/aa/blosum70 -%%DATADIR%%/matrix/aa/blosum75 -%%DATADIR%%/matrix/aa/blosum80 -%%DATADIR%%/matrix/aa/blosum85 -%%DATADIR%%/matrix/aa/DAYHOFF -%%DATADIR%%/matrix/aa/GONNET -%%DATADIR%%/matrix/aa/IDENTITY -%%DATADIR%%/matrix/aa/MATCH -%%DATADIR%%/matrix/aa/PAM10 -%%DATADIR%%/matrix/aa/NUC.4.2 -%%DATADIR%%/matrix/aa/NUC.4.4 -%%DATADIR%%/matrix/aa/PAM100 -%%DATADIR%%/matrix/aa/PAM110 -%%DATADIR%%/matrix/aa/PAM120 -%%DATADIR%%/matrix/aa/PAM130 -%%DATADIR%%/matrix/aa/PAM120.cdi -%%DATADIR%%/matrix/aa/PAM140 -%%DATADIR%%/matrix/aa/PAM150 -%%DATADIR%%/matrix/aa/PAM160 -%%DATADIR%%/matrix/aa/PAM170 -%%DATADIR%%/matrix/aa/PAM160.cdi -%%DATADIR%%/matrix/aa/PAM180 -%%DATADIR%%/matrix/aa/PAM190 -%%DATADIR%%/matrix/aa/PAM20 -%%DATADIR%%/matrix/aa/PAM200 -%%DATADIR%%/matrix/aa/PAM200.cdi -%%DATADIR%%/matrix/aa/PAM210 -%%DATADIR%%/matrix/aa/PAM220 -%%DATADIR%%/matrix/aa/PAM230 -%%DATADIR%%/matrix/aa/PAM240 -%%DATADIR%%/matrix/aa/PAM250 -%%DATADIR%%/matrix/aa/PAM250.cdi -%%DATADIR%%/matrix/aa/PAM260 -%%DATADIR%%/matrix/aa/PAM270 -%%DATADIR%%/matrix/aa/PAM280 -%%DATADIR%%/matrix/aa/PAM290 -%%DATADIR%%/matrix/aa/PAM30 -%%DATADIR%%/matrix/aa/PAM300 -%%DATADIR%%/matrix/aa/PAM310 -%%DATADIR%%/matrix/aa/PAM320 -%%DATADIR%%/matrix/aa/PAM330 -%%DATADIR%%/matrix/aa/PAM340 -%%DATADIR%%/matrix/aa/PAM350 -%%DATADIR%%/matrix/aa/PAM360 -%%DATADIR%%/matrix/aa/PAM370 -%%DATADIR%%/matrix/aa/PAM380 -%%DATADIR%%/matrix/aa/PAM390 -%%DATADIR%%/matrix/aa/PAM40 -%%DATADIR%%/matrix/aa/PAM40.cdi -%%DATADIR%%/matrix/aa/PAM400 -%%DATADIR%%/matrix/aa/PAM410 -%%DATADIR%%/matrix/aa/PAM420 -%%DATADIR%%/matrix/aa/PAM430 -%%DATADIR%%/matrix/aa/PAM440 -%%DATADIR%%/matrix/aa/PAM450 -%%DATADIR%%/matrix/aa/PAM460 -%%DATADIR%%/matrix/aa/PAM470 -%%DATADIR%%/matrix/aa/PAM480 -%%DATADIR%%/matrix/aa/PAM490 -%%DATADIR%%/matrix/aa/PAM50 -%%DATADIR%%/matrix/aa/PAM500 -%%DATADIR%%/matrix/aa/PAM60 -%%DATADIR%%/matrix/aa/PAM70 -%%DATADIR%%/matrix/aa/PAM80 -%%DATADIR%%/matrix/aa/PAM80.cdi -%%DATADIR%%/matrix/aa/PAM90 -%%DATADIR%%/matrix/aa/blosum90 -%%DATADIR%%/matrix/aa/pam120.cdi -%%DATADIR%%/matrix/aa/pam160.cdi -%%DATADIR%%/matrix/aa/dayhoff -%%DATADIR%%/matrix/aa/gonnet -%%DATADIR%%/matrix/aa/identity -%%DATADIR%%/matrix/aa/match -%%DATADIR%%/matrix/aa/pam10 -%%DATADIR%%/matrix/aa/pam100 -%%DATADIR%%/matrix/aa/pam110 -%%DATADIR%%/matrix/aa/pam120 -%%DATADIR%%/matrix/aa/pam130 -%%DATADIR%%/matrix/aa/pam140 -%%DATADIR%%/matrix/aa/pam150 -%%DATADIR%%/matrix/aa/pam160 -%%DATADIR%%/matrix/aa/pam170 -%%DATADIR%%/matrix/aa/pam180 -%%DATADIR%%/matrix/aa/pam190 -%%DATADIR%%/matrix/aa/pam20 -%%DATADIR%%/matrix/aa/pam200 -%%DATADIR%%/matrix/aa/pam250.cdi -%%DATADIR%%/matrix/aa/pam210 -%%DATADIR%%/matrix/aa/pam220 -%%DATADIR%%/matrix/aa/pam230 -%%DATADIR%%/matrix/aa/pam240 -%%DATADIR%%/matrix/aa/pam250 -%%DATADIR%%/matrix/aa/pam40.cdi -%%DATADIR%%/matrix/aa/pam260 -%%DATADIR%%/matrix/aa/pam270 -%%DATADIR%%/matrix/aa/pam280 -%%DATADIR%%/matrix/aa/pam290 -%%DATADIR%%/matrix/aa/pam30 -%%DATADIR%%/matrix/aa/pam300 -%%DATADIR%%/matrix/aa/pam310 -%%DATADIR%%/matrix/aa/pam320 -%%DATADIR%%/matrix/aa/pam330 -%%DATADIR%%/matrix/aa/pam340 -%%DATADIR%%/matrix/aa/pam350 -%%DATADIR%%/matrix/aa/pam360 -%%DATADIR%%/matrix/aa/pam370 -%%DATADIR%%/matrix/aa/pam380 -%%DATADIR%%/matrix/aa/pam390 -%%DATADIR%%/matrix/aa/pam40 -%%DATADIR%%/matrix/aa/pam80.cdi -%%DATADIR%%/matrix/aa/pam400 -%%DATADIR%%/matrix/aa/pam410 -%%DATADIR%%/matrix/aa/pam420 -%%DATADIR%%/matrix/aa/pam430 -%%DATADIR%%/matrix/aa/pam440 -%%DATADIR%%/matrix/aa/pam450 -%%DATADIR%%/matrix/aa/pam460 -%%DATADIR%%/matrix/aa/pam470 -%%DATADIR%%/matrix/aa/pam480 -%%DATADIR%%/matrix/aa/pam490 -%%DATADIR%%/matrix/aa/pam50 -%%DATADIR%%/matrix/aa/pam500 -%%DATADIR%%/matrix/aa/pam60 -%%DATADIR%%/matrix/aa/pam70 -%%DATADIR%%/matrix/aa/pam80 -%%DATADIR%%/matrix/aa/pam90 -%%DATADIR%%/matrix/aa/pam200.cdi -%%DATADIR%%/matrix/aa/PHAT_T70_B66 -%%DATADIR%%/matrix/aa/PHAT_T75_B73 -%%DATADIR%%/matrix/aa/PHAT_T80_B78 -%%DATADIR%%/matrix/aa/PHAT_T85_B82 -%%DATADIR%%/matrix/aa/phat_t70_b66 -%%DATADIR%%/matrix/aa/phat_t75_b73 -%%DATADIR%%/matrix/aa/phat_t80_b78 -%%DATADIR%%/matrix/aa/phat_t85_b82 -%%DATADIR%%/matrix/aa/nuc.4.2 -%%DATADIR%%/matrix/aa/BLOSUM100 -%%DATADIR%%/matrix/nt/PUPY.4.4 -%%DATADIR%%/matrix/nt/IDENTITY.4.2 -%%DATADIR%%/matrix/nt/IDENTITY.4.4 -%%DATADIR%%/matrix/nt/identity.4.2 -%%DATADIR%%/matrix/nt/pupy.4.2 -%%DATADIR%%/matrix/nt/pupy.4.4 -%%DATADIR%%/matrix/nt/PUPY.4.2 -%%DATADIR%%/matrix/nt/identity.4.4 -%%DATADIR%%/matrix/README -%%DATADIR%%/filter/seg -%%DATADIR%%/filter/seg+xnu -%%DATADIR%%/filter/xnu+seg -%%DATADIR%%/filter/nseg -%%DATADIR%%/filter/dust -%%DATADIR%%/filter/nmerge -%%DATADIR%%/filter/xnu -%%DATADIR%%/filter/pmerge -%%DATADIR%%/filter/pseg -%%DATADIR%%/filter/README -%%DATADIR%%/sysblast.sample -%%PORTDOCS%%@dirrm %%DOCSDIR%% -@dirrm %%DATADIR%%/matrix/aa -@dirrm %%DATADIR%%/matrix/nt -@dirrm %%DATADIR%%/matrix -@dirrm %%DATADIR%%/filter -@dirrm %%DATADIR%% diff --git a/biology/embassy/Makefile b/biology/embassy/Makefile deleted file mode 100644 index 1655a08677b5..000000000000 --- a/biology/embassy/Makefile +++ /dev/null @@ -1,131 +0,0 @@ -# Created by: Fernan Aguero <fernan@iib.unsamn.edu.ar> -# $FreeBSD$ - -PORTNAME= embassy -PORTVERSION= 6.2.0 -PORTREVISION= 2 -CATEGORIES= biology -MASTER_SITES= ftp://emboss.open-bio.org/pub/EMBOSS/ -DIST_SUBDIR= emboss - -MAINTAINER= ports@FreeBSD.org -COMMENT= Collection of contributed EMBOSS applications - -BROKEN= does not fetch - -LIB_DEPENDS= libnucleus.so:${PORTSDIR}/biology/emboss - -PREFIX?= ${LOCALBASE}/emboss -NO_MTREE= yes -USE_SUBMAKE= yes -USES= iconv gmake motif -GNU_CONFIGURE= yes -USE_XORG= x11 -USE_LDCONFIG= yes - -OPTIONS_DEFINE= DOMAINATRIX DOMALIGN DOMSEARCH SIGNATURE STRUCTURE \ - EMNU ESIM4 HMMER MEMENEW MSE MYEMBOSS PHYLIPNEW TOPO \ - VIENNA MIRA IPRSCAN CBSTOOLS - -DOMAINATRIX_DESC= Protein domain apps -DOMALIGN_DESC= Protein domain apps -DOMSEARCH_DESC= Protein domain apps -SIGNATURE_DESC= Protein domain apps -STRUCTURE_DESC= Protein domain apps -EMNU_DESC= EMBOSS simple menu -ESIM4_DESC= Align cDNA/EST to genome -HMMER_DESC= HMM alignment and searches -MEMENEW_DESC= Motif detection -MSE_DESC= A multiple sequence screen editor -MYEMBOSS_DESC= Examples for developers of EMBOSS apps -PHYLIPNEW_DESC= Phylogeny inference -TOPO_DESC= Transmembrane display -VIENNA_DESC= RNA folding -MIRA_DESC= Whole Genome shotgun and EST assembler -IPRSCAN_DESC= InterPro scan -CBSTOOLS_DESC= CBS Tools - -OPTIONS_DEFAULT= DOMAINATRIX DOMALIGN DOMSEARCH SIGNATURE STRUCTURE \ - EMNU ESIM4 HMMER MEMENEW MSE MYEMBOSS PHYLIPNEW TOPO \ - VIENNA MIRA IPRSCAN CBSTOOLS - -CPPFLAGS+= -I${PREFIX}/include -I${LOCALBASE}/include -I${LOCALBASE}/emboss/include -LDFLAGS+= -L${PREFIX}/lib -L${LOCALBASE}/lib -L${LOCALBASE}/emboss/lib - -CONFIGURE_ENV= CPPFLAGS="${CPPFLAGS}" LDFLAGS="${LDFLAGS}" - -EMBASSY_WRKDIR= ${WRKSRC}/EMBASSY -DOMAINATRIX_VERSION= 0.1.0 -EMNU_VERSION= 1.05 -ESIM4_VERSION= 1.0.0 -HMMER_VERSION= 2.3.2 -MEMENEW_VERSION= 4.0.0 -MSE_VERSION= 3.0.0 -TOPO_VERSION= 2.0.0 -PHYLIPNEW_VERSION= 3.69 -DOMALIGN_VERSION= 0.1.0 -DOMSEARCH_VERSION= 0.1.0 -SIGNATURE_VERSION= 0.1.0 -STRUCTURE_VERSION= 0.1.0 -MYEMBOSS_VERSION= 6.2.0 -VIENNA_VERSION= 1.7.2 -MIRA_VERSION= 2.8.2 -IPRSCAN_VERSION= 4.3.1 -CBSTOOLS_VERSION= 1.0.0 -EMBASSY_APPS= DOMAINATRIX EMNU ESIM4 HMMER MEMENEW MSE PHYLIPNEW \ - TOPO DOMALIGN DOMSEARCH SIGNATURE STRUCTURE MYEMBOSS \ - VIENNA MIRA IPRSCAN CBSTOOLS - -NO_STAGE= yes -.include <bsd.port.options.mk> - -.for app in ${EMBASSY_APPS} -.if ${PORT_OPTIONS:M${app}} -APPLIST+= ${app} -${app}_WRKSRC= ${EMBASSY_WRKDIR}/${app}-${${app}_VERSION} -${app}_DISTFILE=${app}-${${app}_VERSION}${EXTRACT_SUFX} -DISTFILES+= ${${app}_DISTFILE} -PLIST_${app}= "" -.else -PLIST_${app}= "@comment " -.endif -PLIST_SUB+= PLIST_${app}=${PLIST_${app}} -.endfor - -do-extract: -.for app in ${APPLIST} - @ ${MKDIR} ${EMBASSY_WRKDIR} - @ cd ${EMBASSY_WRKDIR} && ${TAR} ${EXTRACT_BEFORE_ARGS} \ - ${_DISTDIR}/${${app}_DISTFILE} ${EXTRACT_AFTER_ARGS} - @ if [ `id -u` = 0 ]; then \ - ${CHMOD} -R ug-s ${${app}_WRKSRC}; \ - ${CHOWN} -R 0:0 ${${app}_WRKSRC}; \ - fi -.endfor - -post-extract: - @${REINPLACE_CMD} -e 's#emboss_doc##g' ${EMBASSY_WRKDIR}/MIRA-2.8.2/Makefile.in - -post-patch: - @${FIND} ${WRKSRC} -name configure | ${XARGS} ${REINPLACE_CMD} -e 's|echo aout|echo elf|' - -do-configure: -.for app in ${APPLIST} - @ cd ${${app}_WRKSRC} && \ - ${SETENV} ${CONFIGURE_ENV} ./${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS} -.endfor - -do-build: -.for app in ${APPLIST} - @ cd ${${app}_WRKSRC} && \ - ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} -.endfor - -do-install: -.for app in ${APPLIST} - @ cd ${${app}_WRKSRC} && \ - ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_FLAGS} ${MAKEFILE} \ - ${MAKE_ARGS} ${INSTALL_TARGET} -.endfor - -.include <bsd.port.mk> diff --git a/biology/embassy/distinfo b/biology/embassy/distinfo deleted file mode 100644 index c2a406355c43..000000000000 --- a/biology/embassy/distinfo +++ /dev/null @@ -1,34 +0,0 @@ -SHA256 (emboss/DOMAINATRIX-0.1.0.tar.gz) = 53b1633d8a4fec4335ffe96fff309ef2e61b38140dad916b042522e1a48d5e02 -SIZE (emboss/DOMAINATRIX-0.1.0.tar.gz) = 407290 -SHA256 (emboss/EMNU-1.05.tar.gz) = ccad2f9572b2667b2522e47aa8256b2f17e33a31f74f75991424af0c49ca651d -SIZE (emboss/EMNU-1.05.tar.gz) = 368599 -SHA256 (emboss/ESIM4-1.0.0.tar.gz) = 8c02b53105f9bb95fd0acda15133ad4ac736e720df93c06ffaa6fe54b9baad10 -SIZE (emboss/ESIM4-1.0.0.tar.gz) = 406757 -SHA256 (emboss/HMMER-2.3.2.tar.gz) = fd60908ffe8fea41259480701d64c3442a6a469945dbe03fdfa5677b1a3dc6a6 -SIZE (emboss/HMMER-2.3.2.tar.gz) = 559938 -SHA256 (emboss/MEMENEW-4.0.0.tar.gz) = f5dab1527612e060e6230f579b3243e0da2da086df7ba0e280d0efbb99d5d973 -SIZE (emboss/MEMENEW-4.0.0.tar.gz) = 507901 -SHA256 (emboss/MSE-3.0.0.tar.gz) = 1fc5f5313cede53ad95122afeb69b4b588f3b564567bff9855a9691b92eea701 -SIZE (emboss/MSE-3.0.0.tar.gz) = 425691 -SHA256 (emboss/PHYLIPNEW-3.69.tar.gz) = ae0fd57a5b87961d12df8579298d5ec02a147d6678ead4b561dff2c57c5dba67 -SIZE (emboss/PHYLIPNEW-3.69.tar.gz) = 1652212 -SHA256 (emboss/TOPO-2.0.0.tar.gz) = 15f1106800ba803e2c5d79dbfa79b5d521e9ed0ca9da0ceaa77e15366613e915 -SIZE (emboss/TOPO-2.0.0.tar.gz) = 377565 -SHA256 (emboss/DOMALIGN-0.1.0.tar.gz) = 33a12d28c16039663467f34d930b2a0a6ab2ef7d987db94fd8ed4abd02b1bf9f -SIZE (emboss/DOMALIGN-0.1.0.tar.gz) = 430542 -SHA256 (emboss/DOMSEARCH-0.1.0.tar.gz) = af2e408dcd29b9330df7c310d64c888f53d225ebb0bb5402237891fdcdea7ce3 -SIZE (emboss/DOMSEARCH-0.1.0.tar.gz) = 447445 -SHA256 (emboss/SIGNATURE-0.1.0.tar.gz) = e24bda9ff60ef9940f603f4c65b7e5673d6b81ef0c19d53b294197e98bb2497c -SIZE (emboss/SIGNATURE-0.1.0.tar.gz) = 559082 -SHA256 (emboss/STRUCTURE-0.1.0.tar.gz) = c555e1fc16b377109a1bef21116bfe0907709fb2f629d7cbb4add455bc871050 -SIZE (emboss/STRUCTURE-0.1.0.tar.gz) = 521708 -SHA256 (emboss/MYEMBOSS-6.2.0.tar.gz) = 13edbea0d11a14f67631a4cf6c69985f42c97383d8182f8815e294be03c5ebae -SIZE (emboss/MYEMBOSS-6.2.0.tar.gz) = 322935 -SHA256 (emboss/VIENNA-1.7.2.tar.gz) = e2288e6a2f4538cce916033208ab12f0ffb8a92bb1d3ab89fae302b785171fb7 -SIZE (emboss/VIENNA-1.7.2.tar.gz) = 649028 -SHA256 (emboss/MIRA-2.8.2.tar.gz) = 9d2a64fdb1b95bb6e2ac280be3352740e9b5f498f2ff17157374a2ca9744601d -SIZE (emboss/MIRA-2.8.2.tar.gz) = 347282 -SHA256 (emboss/IPRSCAN-4.3.1.tar.gz) = 179513e2473dc31e5b6153c29670773e7bceaaf84315156961baf8f1e292a289 -SIZE (emboss/IPRSCAN-4.3.1.tar.gz) = 345907 -SHA256 (emboss/CBSTOOLS-1.0.0.tar.gz) = 100131d86d4efeafbd63fc712c82bf493e9d174f0bc505e37bdd35ffb56182ff -SIZE (emboss/CBSTOOLS-1.0.0.tar.gz) = 385340 diff --git a/biology/embassy/pkg-descr b/biology/embassy/pkg-descr deleted file mode 100644 index 8a04b6c0ec88..000000000000 --- a/biology/embassy/pkg-descr +++ /dev/null @@ -1,14 +0,0 @@ -EMBASSY is a collection of contributed EMBOSS software. From the web -pages: - - "EMBOSS is GPL licensed. The libraries are under the Lesser GPL (LGPL). - Programs which have been included from third parties who have their own - licencing terms are kept apart under the EMBASSY grouping. - - This allows the EMBOSS libraries to link to other software, and only - requires that software to have an LGPL-compatible licence. Phylip, for - example, fits this model. - - But, to the user they do look exactly like EMBOSS aplications." - -WWW: http://emboss.sourceforge.net/apps/#Embassy diff --git a/biology/embassy/pkg-plist b/biology/embassy/pkg-plist deleted file mode 100644 index ff9b9963614d..000000000000 --- a/biology/embassy/pkg-plist +++ /dev/null @@ -1,515 +0,0 @@ -%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/cathparse.acd -%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainnr.acd -%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainreso.acd -%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainseqs.acd -%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainsse.acd -%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scopparse.acd -%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/ssematch.acd -%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/programs/text/cathparse.txt -%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/programs/text/domainnr.txt -%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/programs/text/domainreso.txt -%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/programs/text/domainseqs.txt -%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/programs/text/domainsse.txt -%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/programs/text/scopparse.txt -%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/programs/text/ssematch.txt -%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/index.html -%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/cathparse.html -%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/domainnr.html -%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/domainreso.html -%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/domainseqs.html -%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/domainsse.html -%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/scopparse.html -%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/ssematch.html -%%PLIST_DOMAINATRIX%%bin/cathparse -%%PLIST_DOMAINATRIX%%bin/domainnr -%%PLIST_DOMAINATRIX%%bin/domainreso -%%PLIST_DOMAINATRIX%%bin/domainseqs 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-%%PLIST_DOMALIGN%%share/EMBOSS/doc/html/embassy/domalign/seqalign.html -%%PLIST_DOMALIGN%%@dirrm share/EMBOSS/doc/html/embassy/domalign -%%PLIST_DOMALIGN%%bin/allversusall -%%PLIST_DOMALIGN%%bin/domainalign -%%PLIST_DOMALIGN%%bin/domainrep -%%PLIST_DOMALIGN%%bin/seqalign -%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqnr.acd -%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqsearch.acd -%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqfraggle.acd -%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqsort.acd -%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqwords.acd -%%PLIST_DOMSEARCH%%share/EMBOSS/doc/programs/text/seqfraggle.txt -%%PLIST_DOMSEARCH%%share/EMBOSS/doc/programs/text/seqnr.txt -%%PLIST_DOMSEARCH%%share/EMBOSS/doc/programs/text/seqsearch.txt -%%PLIST_DOMSEARCH%%share/EMBOSS/doc/programs/text/seqsort.txt -%%PLIST_DOMSEARCH%%share/EMBOSS/doc/programs/text/seqwords.txt -%%PLIST_DOMSEARCH%%share/EMBOSS/doc/html/embassy/domsearch/index.html -%%PLIST_DOMSEARCH%%share/EMBOSS/doc/html/embassy/domsearch/seqfraggle.html -%%PLIST_DOMSEARCH%%share/EMBOSS/doc/html/embassy/domsearch/seqnr.html -%%PLIST_DOMSEARCH%%share/EMBOSS/doc/html/embassy/domsearch/seqsearch.html -%%PLIST_DOMSEARCH%%share/EMBOSS/doc/html/embassy/domsearch/seqsort.html -%%PLIST_DOMSEARCH%%share/EMBOSS/doc/html/embassy/domsearch/seqwords.html -%%PLIST_DOMSEARCH%%@dirrm share/EMBOSS/doc/html/embassy/domsearch -%%PLIST_DOMSEARCH%%bin/seqnr -%%PLIST_DOMSEARCH%%bin/seqsearch -%%PLIST_DOMSEARCH%%bin/seqfraggle -%%PLIST_DOMSEARCH%%bin/seqsort -%%PLIST_DOMSEARCH%%bin/seqwords -%%PLIST_SIGNATURE%%share/EMBOSS/acd/libgen.acd -%%PLIST_SIGNATURE%%share/EMBOSS/acd/matgen3d.acd -%%PLIST_SIGNATURE%%share/EMBOSS/acd/rocplot.acd -%%PLIST_SIGNATURE%%share/EMBOSS/acd/rocon.acd -%%PLIST_SIGNATURE%%share/EMBOSS/acd/siggen.acd -%%PLIST_SIGNATURE%%share/EMBOSS/acd/siggenlig.acd -%%PLIST_SIGNATURE%%share/EMBOSS/acd/sigscan.acd -%%PLIST_SIGNATURE%%share/EMBOSS/acd/sigscanlig.acd -%%PLIST_SIGNATURE%%share/EMBOSS/doc/programs/text/libgen.txt 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-%%PLIST_SIGNATURE%%share/EMBOSS/doc/html/embassy/signature/sigscan.html -%%PLIST_SIGNATURE%%share/EMBOSS/doc/html/embassy/signature/sigscanlig.html -%%PLIST_SIGNATURE%%@dirrm share/EMBOSS/doc/html/embassy/signature -%%PLIST_SIGNATURE%%bin/libgen -%%PLIST_SIGNATURE%%bin/matgen3d -%%PLIST_SIGNATURE%%bin/rocplot -%%PLIST_SIGNATURE%%bin/rocon -%%PLIST_SIGNATURE%%bin/siggen -%%PLIST_SIGNATURE%%bin/siggenlig -%%PLIST_SIGNATURE%%bin/sigscan -%%PLIST_SIGNATURE%%bin/sigscanlig -%%PLIST_STRUCTURE%%share/EMBOSS/acd/contacts.acd -%%PLIST_STRUCTURE%%share/EMBOSS/acd/domainer.acd -%%PLIST_STRUCTURE%%share/EMBOSS/acd/hetparse.acd -%%PLIST_STRUCTURE%%share/EMBOSS/acd/interface.acd -%%PLIST_STRUCTURE%%share/EMBOSS/acd/pdbparse.acd -%%PLIST_STRUCTURE%%share/EMBOSS/acd/pdbplus.acd -%%PLIST_STRUCTURE%%share/EMBOSS/acd/pdbtosp.acd -%%PLIST_STRUCTURE%%share/EMBOSS/acd/sites.acd -%%PLIST_STRUCTURE%%share/EMBOSS/doc/programs/text/contacts.txt -%%PLIST_STRUCTURE%%share/EMBOSS/doc/programs/text/domainer.txt 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-%%PLIST_ESIM4%%bin/esim4 -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmcalibrate.acd -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmconvert.acd -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmemit.acd -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmfetch.acd -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmindex.acd -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmbuild.acd -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmalign.acd -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmpfam.acd -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmsearch.acd -%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmalign.txt -%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmbuild.txt -%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmcalibrate.txt -%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmconvert.txt -%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmemit.txt -%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmfetch.txt -%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmindex.txt -%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmpfam.txt 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-@dirrm share/EMBOSS/doc/html/embassy -@dirrmtry share/EMBOSS/doc/html -@dirrmtry share/EMBOSS/doc -@dirrmtry share/EMBOSS -@dirrmtry share diff --git a/biology/pymol/Makefile b/biology/pymol/Makefile deleted file mode 100644 index 11d56ac81f93..000000000000 --- a/biology/pymol/Makefile +++ /dev/null @@ -1,49 +0,0 @@ -# Created by: Nakata Maho <chat95@mbox.kyoto-inet.or.jp> -# $FreeBSD$ - -PORTNAME= pymol -PORTVERSION= ${VERSION}.${SVNREVISION} -PORTREVISION= 3 -CATEGORIES= biology python -MASTER_SITES= ${MASTER_SITE_LOCAL:S|%SUBDIR%|maho/pymol|} - -MAINTAINER= ports@FreeBSD.org -COMMENT= Free and Open-Source molecular modeling system - -BUILD_DEPENDS= ${PYNUMERIC} -RUN_DEPENDS= ${PYNUMERIC} \ - ${PYTHON_SITELIBDIR}/Pmw:${PORTSDIR}/x11-toolkits/py-Pmw -LIB_DEPENDS= libpng15.so:${PORTSDIR}/graphics/png \ - libfreetype.so:${PORTSDIR}/print/freetype2 - -VERSION= 1.5.0.1 -SVNREVISION= 3978 - -WRKSRC= ${WRKDIR}/pymol-${PORTVERSION} -USE_GL= glut glew -USES= gmake tar:bzip2 -USE_PYTHON= yes -PLIST_SUB= PYMOL_VER=${VERSION} PYTHON_VER=${PYTHON_VER} - -NO_STAGE= yes -pre-build: - @${REINPLACE_CMD} -e "s+%%LOCALBASE%%+${LOCALBASE}+" ${WRKSRC}/setup.py - -#do build process actually installs some files, so omitted. -do-build: - -do-install: - @(cd ${BUILD_WRKSRC}; ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} ${PYSETUP} install) - @(cd ${BUILD_WRKSRC}; ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} setup2.py install) - @${INSTALL_SCRIPT} ${WRKSRC}/pymol ${PREFIX}/bin/pymol - -#maintainance -do-fetch-svn: - #svn ls https://pymol.svn.sourceforge.net/svnroot/pymol/tags - #http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/ - ${RM} -rf pymol-${VERSION}.${SVNREVISION} - svn -r ${SVNREVISION} export http://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol-${VERSION}.${SVNREVISION} - tar cvfj pymol-${VERSION}.${SVNREVISION}.tar.bz2 pymol-${VERSION}.${SVNREVISION} - scp pymol-${VERSION}.${SVNREVISION}.tar.bz2 freefall.freebsd.org:public_distfiles/pymol/ - -.include <bsd.port.mk> diff --git a/biology/pymol/distinfo b/biology/pymol/distinfo deleted file mode 100644 index 509273172d80..000000000000 --- a/biology/pymol/distinfo +++ /dev/null @@ -1,2 +0,0 @@ -SHA256 (pymol-1.5.0.1.3978.tar.bz2) = 76ff4a6bc126f3fd4dccb62c2345fea3b2a007ecc687d89f7fe21b8f5a0496fc -SIZE (pymol-1.5.0.1.3978.tar.bz2) = 9730397 diff --git a/biology/pymol/files/patch-setup.py b/biology/pymol/files/patch-setup.py deleted file mode 100644 index 105d89d8a732..000000000000 --- a/biology/pymol/files/patch-setup.py +++ /dev/null @@ -1,31 +0,0 @@ ---- setup.py 2012-02-14 04:02:02.000000000 +0900 -+++ setup.py 2012-02-15 13:09:38.000000000 +0900 -@@ -159,7 +159,8 @@ - "layer3", - "layer4", - "layer5", -- "/usr/include/freetype2", -+ "%%LOCALBASE%%/include/freetype2", -+ "%%LOCALBASE%%/include", - # VMD plugin support - # "contrib/uiuc/plugins/include", - # "contrib/uiuc/plugins/molfile_plugin/src", -@@ -181,7 +181,7 @@ - "GLU", - "glut", - "GLEW"] -- lib_dirs = [ "/usr/X11R6/lib64", ] -+ lib_dirs = [ "%%LOCALBASE%%/lib", ] - def_macros = [ ("_PYMOL_MODULE",None), - ("_PYMOL_INLINE",None), - ("_PYMOL_FREETYPE",None), -@@ -201,7 +202,7 @@ - "-funroll-loops", - "-O3", - "-g" ] -- ext_link_args = [] -+ ext_link_args = [ "-L%%LOCALBASE%%/lib" ] - - - distribution = setup ( # Distribution meta-data - diff --git a/biology/pymol/pkg-descr b/biology/pymol/pkg-descr deleted file mode 100644 index dfd8cdfb4d4f..000000000000 --- a/biology/pymol/pkg-descr +++ /dev/null @@ -1,9 +0,0 @@ -PyMOL is a molecular graphics system with an embedded Python interpreter -designed for real-time visualization and rapid generation of -high-quality molecular graphics images and animations. It is fully extensible -and available free to everyone via the "Python" license. -PyMOL can be used to create images and animations with unprecedented ease. -It can also perform many other valuable tasks (such as editing PDB files) -to assist you in your research. - -WWW: http://pymol.sourceforge.net/ diff --git a/biology/pymol/pkg-plist b/biology/pymol/pkg-plist deleted file mode 100644 index fb7eabf7b538..000000000000 --- a/biology/pymol/pkg-plist +++ /dev/null @@ -1,854 +0,0 @@ -bin/pymol -%%PYTHON_SITELIBDIR%%/chempy/__init__.py -%%PYTHON_SITELIBDIR%%/chempy/__init__.pyc -%%PYTHON_SITELIBDIR%%/chempy/arc.py -%%PYTHON_SITELIBDIR%%/chempy/arc.pyc -%%PYTHON_SITELIBDIR%%/chempy/bmin/__init__.py -%%PYTHON_SITELIBDIR%%/chempy/bmin/__init__.pyc -%%PYTHON_SITELIBDIR%%/chempy/bmin/commands.py -%%PYTHON_SITELIBDIR%%/chempy/bmin/commands.pyc -%%PYTHON_SITELIBDIR%%/chempy/bmin/realtime.py -%%PYTHON_SITELIBDIR%%/chempy/bmin/realtime.pyc -%%PYTHON_SITELIBDIR%%/chempy/bmin/state.py 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