svn commit: r502015 - in head/biology: . hhsuite hhsuite/files
Yuri Victorovich
yuri at FreeBSD.org
Sun May 19 06:52:41 UTC 2019
Author: yuri
Date: Sun May 19 06:52:38 2019
New Revision: 502015
URL: https://svnweb.freebsd.org/changeset/ports/502015
Log:
New port: biology/hhsuite: Remote protein homology detection suite
Added:
head/biology/hhsuite/
head/biology/hhsuite/Makefile (contents, props changed)
head/biology/hhsuite/distinfo (contents, props changed)
head/biology/hhsuite/files/
head/biology/hhsuite/files/patch-data_CMakeLists.txt (contents, props changed)
head/biology/hhsuite/files/patch-scripts_CMakeLists.txt (contents, props changed)
head/biology/hhsuite/files/patch-src_cs_getopt__pp.cc (contents, props changed)
head/biology/hhsuite/pkg-descr (contents, props changed)
head/biology/hhsuite/pkg-plist (contents, props changed)
Modified:
head/biology/Makefile
Modified: head/biology/Makefile
==============================================================================
--- head/biology/Makefile Sun May 19 06:08:58 2019 (r502014)
+++ head/biology/Makefile Sun May 19 06:52:38 2019 (r502015)
@@ -49,6 +49,7 @@
SUBDIR += graphlan
SUBDIR += grappa
SUBDIR += groopm
+ SUBDIR += hhsuite
SUBDIR += hisat2
SUBDIR += hmmer
SUBDIR += htslib
Added: head/biology/hhsuite/Makefile
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/hhsuite/Makefile Sun May 19 06:52:38 2019 (r502015)
@@ -0,0 +1,26 @@
+# $FreeBSD$
+
+PORTNAME= hhsuite
+DISTVERSIONPREFIX= v
+DISTVERSION= 3.2.0
+CATEGORIES= biology science
+
+MAINTAINER= yuri at FreeBSD.org
+COMMENT= Remote protein homology detection suite
+
+LICENSE= GPLv3
+LICENSE_FILE= ${WRKSRC}/LICENSE
+
+BUILD_DEPENDS= openmpi>0:net/openmpi
+LIB_DEPENDS= libomp.so:devel/openmp
+RUN_DEPENDS= openmpi>0:net/openmpi
+
+USES= cmake perl5 python shebangfix
+SHEBANG_GLOB= *.pl *.py
+USE_GITHUB= yes
+GH_ACCOUNT= soedinglab
+GH_PROJECT= hh-suite
+
+LDFLAGS+= -Wl,-rpath,${LOCALBASE}/mpi/openmpi/lib -L${LOCALBASE}/mpi/openmpi/lib -lmpi # force linking to openmpi, and not to mpich
+
+.include <bsd.port.mk>
Added: head/biology/hhsuite/distinfo
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/hhsuite/distinfo Sun May 19 06:52:38 2019 (r502015)
@@ -0,0 +1,3 @@
+TIMESTAMP = 1558244086
+SHA256 (soedinglab-hh-suite-v3.2.0_GH0.tar.gz) = 6b870dcfbc1ffb9dd664a45415fcd13cf5970f49d1c7b824160c260fa138e6d6
+SIZE (soedinglab-hh-suite-v3.2.0_GH0.tar.gz) = 6273589
Added: head/biology/hhsuite/files/patch-data_CMakeLists.txt
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/hhsuite/files/patch-data_CMakeLists.txt Sun May 19 06:52:38 2019 (r502015)
@@ -0,0 +1,11 @@
+--- data/CMakeLists.txt.orig 2019-05-19 05:46:02 UTC
++++ data/CMakeLists.txt
+@@ -7,7 +7,7 @@ INSTALL(FILES
+ do_not_delete.pin
+ do_not_delete.psq
+ PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ
+- DESTINATION data
++ DESTINATION ${CMAKE_INSTALL_PREFIX}/share/hhsuite/data
+ )
+
+ include(ResourceCompiler)
Added: head/biology/hhsuite/files/patch-scripts_CMakeLists.txt
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/hhsuite/files/patch-scripts_CMakeLists.txt Sun May 19 06:52:38 2019 (r502015)
@@ -0,0 +1,9 @@
+--- scripts/CMakeLists.txt.orig 2019-05-19 05:44:58 UTC
++++ scripts/CMakeLists.txt
+@@ -21,5 +21,5 @@ INSTALL(PROGRAMS
+ reformat.pl
+ renumberpdb.pl
+ splitfasta.pl
+- DESTINATION scripts
++ DESTINATION ${CMAKE_INSTALL_PREFIX}/share/hhsuite/scripts
+ )
Added: head/biology/hhsuite/files/patch-src_cs_getopt__pp.cc
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/hhsuite/files/patch-src_cs_getopt__pp.cc Sun May 19 06:52:38 2019 (r502015)
@@ -0,0 +1,11 @@
+--- src/cs/getopt_pp.cc.orig 2019-05-19 05:36:03 UTC
++++ src/cs/getopt_pp.cc
+@@ -21,7 +21,7 @@
+ #include <unistd.h>
+ #include "getopt_pp.h"
+
+-#ifdef __APPLE__
++#if defined(__APPLE__) || defined(__FreeBSD__)
+ extern char** environ;
+ #endif
+
Added: head/biology/hhsuite/pkg-descr
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/hhsuite/pkg-descr Sun May 19 06:52:38 2019 (r502015)
@@ -0,0 +1,8 @@
+SIMD-vectorized implementation of the Viterbi algorithm for profile HMM
+alignment and introduced various other speed-ups. This accelerated HHsearch by a
+factor 4 and HHblits by a factor 2 over the previous version 2.0.16. HHblits3 is
+~10x faster than PSI-BLAST and ~20x faster than HMMER3. Jobs to perform HHsearch
+and HHblits searches with many query profile HMMs can be parallelized over cores
+and over servers in a cluster using OpenMP and message passing interface (MPI).
+
+WWW: https://github.com/soedinglab/hh-suite
Added: head/biology/hhsuite/pkg-plist
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/hhsuite/pkg-plist Sun May 19 06:52:38 2019 (r502015)
@@ -0,0 +1,59 @@
+bin/a3m_database_extract
+bin/a3m_database_filter
+bin/a3m_database_reduce
+bin/a3m_extract
+bin/a3m_reduce
+bin/cstranslate
+bin/cstranslate_mpi
+bin/ffindex_apply
+bin/ffindex_apply_mpi
+bin/ffindex_build
+bin/ffindex_from_fasta
+bin/ffindex_from_fasta_with_split
+bin/ffindex_get
+bin/ffindex_modify
+bin/ffindex_order
+bin/ffindex_reduce
+bin/ffindex_unpack
+bin/hhalign
+bin/hhalign_mpi
+bin/hhalign_omp
+bin/hhblits
+bin/hhblits_ca3m
+bin/hhblits_mpi
+bin/hhblits_omp
+bin/hhconsensus
+bin/hhfilter
+bin/hhmake
+bin/hhsearch
+bin/hhsearch_mpi
+bin/hhsearch_omp
+%%DATADIR%%/data/context_data.crf
+%%DATADIR%%/data/context_data.lib
+%%DATADIR%%/data/cs219.lib
+%%DATADIR%%/data/do_not_delete
+%%DATADIR%%/data/do_not_delete.phr
+%%DATADIR%%/data/do_not_delete.pin
+%%DATADIR%%/data/do_not_delete.psq
+%%DATADIR%%/scripts/Align.pm
+%%DATADIR%%/scripts/HHPaths.pm
+%%DATADIR%%/scripts/a3m.py
+%%DATADIR%%/scripts/addss.pl
+%%DATADIR%%/scripts/check_a3m.py
+%%DATADIR%%/scripts/cif2fasta.py
+%%DATADIR%%/scripts/create_profile_from_hhm.pl
+%%DATADIR%%/scripts/create_profile_from_hmmer.pl
+%%DATADIR%%/scripts/ffindex.py
+%%DATADIR%%/scripts/get_a3m_size.py
+%%DATADIR%%/scripts/hh_reader.py
+%%DATADIR%%/scripts/hhmakemodel.pl
+%%DATADIR%%/scripts/hhmakemodel.py
+%%DATADIR%%/scripts/hhsuitedb.py
+%%DATADIR%%/scripts/mergeali.pl
+%%DATADIR%%/scripts/multithread.pl
+%%DATADIR%%/scripts/pdb2fasta.pl
+%%DATADIR%%/scripts/pdbfilter.pl
+%%DATADIR%%/scripts/pdbfilter.py
+%%DATADIR%%/scripts/reformat.pl
+%%DATADIR%%/scripts/renumberpdb.pl
+%%DATADIR%%/scripts/splitfasta.pl
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