diff options
| author | Jason W. Bacon <jwb@FreeBSD.org> | 2019-01-12 15:53:00 +0000 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2019-01-12 15:53:00 +0000 |
| commit | f03dcf6979a319e06f698a2cbaaa81f9176294ba (patch) | |
| tree | 3aeb6434a4bdbae91832fe9b622710416bce4633 /biology | |
| parent | c9f2c7ed76739ed71de23bcfd324df0fb802afd1 (diff) | |
Notes
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/stacks/Makefile | 11 | ||||
| -rw-r--r-- | biology/stacks/distinfo | 6 | ||||
| -rw-r--r-- | biology/stacks/files/patch-htslib_Makefile | 20 | ||||
| -rw-r--r-- | biology/stacks/pkg-plist | 15 |
4 files changed, 14 insertions, 38 deletions
diff --git a/biology/stacks/Makefile b/biology/stacks/Makefile index 2ccf32888998..d7e0d0938118 100644 --- a/biology/stacks/Makefile +++ b/biology/stacks/Makefile @@ -1,9 +1,8 @@ # $FreeBSD$ PORTNAME= stacks -DISTVERSION= 1.48 -PORTREVISION= 3 -CATEGORIES= biology +DISTVERSION= 2.3 +CATEGORIES= biology perl5 python MASTER_SITES= http://catchenlab.life.illinois.edu/stacks/source/ MAINTAINER= jwb@FreeBSD.org @@ -13,7 +12,9 @@ LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE USES= compiler:openmp gmake python shebangfix -SHEBANG_FILES= scripts/*.pl scripts/*.py + +SHEBANG_FILES= scripts/*.pl scripts/*.py \ + scripts/stacks-integrate-alignments scripts/stacks-gdb GNU_CONFIGURE= yes LDFLAGS+= -lpthread @@ -21,7 +22,7 @@ LDFLAGS+= -lpthread .include <bsd.port.pre.mk> .if ${ARCH} != amd64 && ${ARCH} != i386 -USE_GCC= yes +USE_GCC= yes .endif .include <bsd.port.post.mk> diff --git a/biology/stacks/distinfo b/biology/stacks/distinfo index e32def18090a..d8c244d985e0 100644 --- a/biology/stacks/distinfo +++ b/biology/stacks/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1520376299 -SHA256 (stacks-1.48.tar.gz) = e9f6251f5f609f9dd0bb1de17a51f69ce1a9af531548c4d2456a89783b1dcd1e -SIZE (stacks-1.48.tar.gz) = 895195 +TIMESTAMP = 1547306940 +SHA256 (stacks-2.3.tar.gz) = 2a5befaf11ca2f191afcd42a3a3392290d6a116d7fe737b69a2c4d5b77f40c99 +SIZE (stacks-2.3.tar.gz) = 10962586 diff --git a/biology/stacks/files/patch-htslib_Makefile b/biology/stacks/files/patch-htslib_Makefile deleted file mode 100644 index 7a1235d9f2a2..000000000000 --- a/biology/stacks/files/patch-htslib_Makefile +++ /dev/null @@ -1,20 +0,0 @@ ---- htslib/Makefile.orig 2016-09-16 15:40:03 UTC -+++ htslib/Makefile -@@ -22,13 +22,13 @@ - # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER - # DEALINGS IN THE SOFTWARE. - --CC = gcc --AR = ar --RANLIB = ranlib -+CC ?= gcc -+AR ?= ar -+RANLIB ?= ranlib - - CPPFLAGS = - # TODO: probably update cram code to make it compile cleanly with -Wc++-compat --CFLAGS = -g -Wall -O2 -+CFLAGS ?= -g -Wall -O2 - EXTRA_CFLAGS_PIC = -fpic - LDFLAGS = - LIBS = diff --git a/biology/stacks/pkg-plist b/biology/stacks/pkg-plist index 4f85229d528c..6660e468dce5 100644 --- a/biology/stacks/pkg-plist +++ b/biology/stacks/pkg-plist @@ -2,24 +2,19 @@ bin/clone_filter bin/count_fixed_catalog_snps.py bin/cstacks bin/denovo_map.pl -bin/exec_velvet.pl -bin/export_sql.pl -bin/genotypes -bin/index_radtags.pl +bin/gstacks bin/integrate_alignments.py bin/kmer_filter -bin/load_radtags.pl -bin/load_sequences.pl bin/phasedstacks bin/populations bin/process_radtags bin/process_shortreads -bin/pstacks bin/ref_map.pl -bin/rxstacks -bin/sort_read_pairs.pl bin/sstacks -bin/stacks_export_notify.pl +bin/stacks-dist-extract +bin/stacks-gdb +bin/stacks-integrate-alignments +bin/tsv2bam bin/ustacks %%DATADIR%%/php/CatalogClass.php %%DATADIR%%/php/Locus.php |