Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 466047) +++ head/biology/Makefile (revision 466048) @@ -1,123 +1,124 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += ariadne SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += blat SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += chemeq SUBDIR += clustalw SUBDIR += consed SUBDIR += crux SUBDIR += diamond SUBDIR += emboss SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += fluctuate SUBDIR += garlic SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += grappa SUBDIR += hmmer SUBDIR += htslib SUBDIR += iolib SUBDIR += iqtree SUBDIR += jalview SUBDIR += jellyfish SUBDIR += kallisto SUBDIR += lagan SUBDIR += lamarc SUBDIR += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += molden SUBDIR += mopac SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-toolkit SUBDIR += njplot SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Coordinate SUBDIR += p5-Bio-Das SUBDIR += p5-Bio-Das-Lite SUBDIR += p5-Bio-FeatureIO SUBDIR += p5-Bio-GFF3 SUBDIR += p5-Bio-Glite SUBDIR += p5-Bio-Graphics SUBDIR += p5-Bio-MAGETAB SUBDIR += p5-Bio-NEXUS SUBDIR += p5-Bio-Phylo SUBDIR += p5-Bio-SCF SUBDIR += p5-BioPerl SUBDIR += p5-BioPerl-Run SUBDIR += p5-TrimGalore SUBDIR += p5-transdecoder SUBDIR += paml SUBDIR += phrap SUBDIR += phred SUBDIR += phylip SUBDIR += phyml SUBDIR += plink SUBDIR += plinkseq SUBDIR += primer3 SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-cutadapt SUBDIR += py-macs2 SUBDIR += py-pysam SUBDIR += pycogent SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += samtools SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqio SUBDIR += seqtools SUBDIR += sim4 SUBDIR += slclust SUBDIR += ssaha + SUBDIR += stacks SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tinker SUBDIR += treepuzzle SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += vcftools SUBDIR += velvet SUBDIR += wise SUBDIR += xmolwt .include Index: head/biology/stacks/Makefile =================================================================== --- head/biology/stacks/Makefile (nonexistent) +++ head/biology/stacks/Makefile (revision 466048) @@ -0,0 +1,20 @@ +# $FreeBSD$ + +PORTNAME= stacks +DISTVERSION= 1.48 +CATEGORIES= biology +MASTER_SITES= http://catchenlab.life.illinois.edu/stacks/source/ + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Software pipeline for building loci from short-read sequences + +LICENSE= GPLv2 +LICENSE_FILE= ${WRKSRC}/LICENSE + +USES= gmake python shebangfix +SHEBANG_FILES= scripts/*.pl scripts/*.py +GNU_CONFIGURE= yes + +LDFLAGS+= -lpthread + +.include Property changes on: head/biology/stacks/Makefile ___________________________________________________________________ Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:keywords ## -0,0 +1 ## +FreeBSD=%H \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/stacks/distinfo =================================================================== --- head/biology/stacks/distinfo (nonexistent) +++ head/biology/stacks/distinfo (revision 466048) @@ -0,0 +1,3 @@ +TIMESTAMP = 1520376299 +SHA256 (stacks-1.48.tar.gz) = e9f6251f5f609f9dd0bb1de17a51f69ce1a9af531548c4d2456a89783b1dcd1e +SIZE (stacks-1.48.tar.gz) = 895195 Property changes on: head/biology/stacks/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/stacks/files/patch-htslib_Makefile =================================================================== --- head/biology/stacks/files/patch-htslib_Makefile (nonexistent) +++ head/biology/stacks/files/patch-htslib_Makefile (revision 466048) @@ -0,0 +1,20 @@ +--- 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 = Property changes on: head/biology/stacks/files/patch-htslib_Makefile ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/stacks/pkg-descr =================================================================== --- head/biology/stacks/pkg-descr (nonexistent) +++ head/biology/stacks/pkg-descr (revision 466048) @@ -0,0 +1,6 @@ +Stacks is a software pipeline for building loci from short-read sequences, such +as those generated on the Illumina platform. Stacks was developed to work with +restriction enzyme-based data, such as RAD-seq, for the purpose of building +genetic maps and conducting population genomics and phylogeography. + +WWW: http://catchenlab.life.illinois.edu/stacks/ Property changes on: head/biology/stacks/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/stacks/pkg-message =================================================================== --- head/biology/stacks/pkg-message (nonexistent) +++ head/biology/stacks/pkg-message (revision 466048) @@ -0,0 +1,16 @@ +=== + +If you would like to use the stacks web interface, follow the instructions at: + + http://catchenlab.life.illinois.edu/stacks/manual-v1/#install + +You will need to install databases/p5-DBD-mysql to allow the optional +wrapper scripts to interact with the database server. + +To set up the web server, you will need an apache server such as www/apache24, +MySQL server and client packages such as databases/mysql56-client and +databases/mysql56-server, and PHP interface modules such as +databases/php56-mysql (php56 will be automatically installed as a dependency), +and lastly textproc/p5-Spreadsheet-WriteExcel. + +=== Property changes on: head/biology/stacks/pkg-message ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/stacks/pkg-plist =================================================================== --- head/biology/stacks/pkg-plist (nonexistent) +++ head/biology/stacks/pkg-plist (revision 466048) @@ -0,0 +1,70 @@ +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/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/ustacks +%%DATADIR%%/php/CatalogClass.php +%%DATADIR%%/php/Locus.php +%%DATADIR%%/php/ajax.js +%%DATADIR%%/php/annotate.js +%%DATADIR%%/php/annotate_marker.php +%%DATADIR%%/php/catalog.php +%%DATADIR%%/php/catalog_genotypes.php +%%DATADIR%%/php/constants.php.dist +%%DATADIR%%/php/correct_genotype.php +%%DATADIR%%/php/correct_genotypes.php +%%DATADIR%%/php/db_functions.php +%%DATADIR%%/php/export.js +%%DATADIR%%/php/export_batch.php +%%DATADIR%%/php/fst_view.php +%%DATADIR%%/php/hapstat_view.php +%%DATADIR%%/php/header.php +%%DATADIR%%/php/images/caret-d.png +%%DATADIR%%/php/images/caret-u.png +%%DATADIR%%/php/images/excel_icon.png +%%DATADIR%%/php/images/l-arrow-disabled.png +%%DATADIR%%/php/images/l-arrow.png +%%DATADIR%%/php/images/r-arrow-disabled.png +%%DATADIR%%/php/images/r-arrow.png +%%DATADIR%%/php/images/stacks_bg.png +%%DATADIR%%/php/images/stacks_logo_rev_small.png +%%DATADIR%%/php/index.php +%%DATADIR%%/php/last_modified.php +%%DATADIR%%/php/phist_view.php +%%DATADIR%%/php/pop_view.php +%%DATADIR%%/php/population_view.js +%%DATADIR%%/php/samples.php +%%DATADIR%%/php/sequence_blast.php +%%DATADIR%%/php/stack_view.php +%%DATADIR%%/php/stacks.css +%%DATADIR%%/php/stacks.js +%%DATADIR%%/php/stacks_functions.php +%%DATADIR%%/php/sumstat_view.php +%%DATADIR%%/php/tag.php +%%DATADIR%%/php/tags.php +%%DATADIR%%/php/version.php +%%DATADIR%%/php/view_sequence.php +%%DATADIR%%/sql/catalog_index.sql +%%DATADIR%%/sql/chr_index.sql +%%DATADIR%%/sql/mysql.cnf.dist +%%DATADIR%%/sql/stacks.sql +%%DATADIR%%/sql/tag_index.sql +@dir %%DATADIR%%/php/export Property changes on: head/biology/stacks/pkg-plist ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property