Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 512645) +++ head/biology/Makefile (revision 512646) @@ -1,173 +1,174 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += abyss SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += bolt-lmm SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += checkm SUBDIR += chemeq SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += consed SUBDIR += cufflinks SUBDIR += cytoscape SUBDIR += ddocent SUBDIR += diamond SUBDIR += dsr-pdb SUBDIR += emboss SUBDIR += exonerate SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastp SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += figtree SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gatk SUBDIR += gemma SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += graphlan SUBDIR += grappa SUBDIR += groopm SUBDIR += haplohseq SUBDIR += hhsuite SUBDIR += hisat2 SUBDIR += hmmer SUBDIR += htslib SUBDIR += hyphy SUBDIR += igv SUBDIR += infernal SUBDIR += iolib SUBDIR += iqtree SUBDIR += jalview SUBDIR += jellyfish SUBDIR += kallisto SUBDIR += lagan SUBDIR += lamarc SUBDIR += libbigwig SUBDIR += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += minimap2 SUBDIR += molden SUBDIR += mopac SUBDIR += mothur SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-cxx-toolkit SUBDIR += ncbi-toolkit SUBDIR += ngs-sdk SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Cluster 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 += pbbam SUBDIR += pbcopper SUBDIR += pbseqan SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred SUBDIR += phylip SUBDIR += phyml SUBDIR += plinkseq SUBDIR += primer3 SUBDIR += prodigal SUBDIR += prodigy-lig SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-Genesis-PyAPI SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-cutadapt SUBDIR += py-dnaio SUBDIR += py-fastTSNE SUBDIR += py-gffutils SUBDIR += py-gtfparse SUBDIR += py-loompy SUBDIR += py-macs2 + SUBDIR += py-multiqc SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pyfaidx SUBDIR += py-pysam SUBDIR += py-xenaPython SUBDIR += pycogent SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += samtools SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqio SUBDIR += seqtk SUBDIR += seqtools SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += stacks SUBDIR += star SUBDIR += stringtie SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tabixpp SUBDIR += treekin SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += unanimity SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += viennarna SUBDIR += vsearch SUBDIR += wise .include Index: head/biology/py-multiqc/Makefile =================================================================== --- head/biology/py-multiqc/Makefile (nonexistent) +++ head/biology/py-multiqc/Makefile (revision 512646) @@ -0,0 +1,36 @@ +# $FreeBSD$ + +PORTNAME= multiqc +DISTVERSION= 1.7 +CATEGORIES= biology python +MASTER_SITES= CHEESESHOP +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Aggregate bioinformatics analysis reports across samples and tools + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE + +RUN_DEPENDS= ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}click>0:devel/py-click@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}future>0.14.0:devel/py-future@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}matplotlib>=2.1.1:math/py-matplotlib@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}markdown>0:textproc/py-markdown@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}yaml>0:devel/py-yaml@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}requests>:www/py-requests@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}simplejson>0:devel/py-simplejson@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}Jinja2>=2.9:devel/py-Jinja2@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}lzstring>0:archivers/py-lzstring@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}spectra>=0.0.10:graphics/py-spectra@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}colormath>0:math/py-colormath@${PY_FLAVOR} + +USES= python +USE_PYTHON= autoplist concurrent distutils + +NO_ARCH= yes + +post-patch: + @${RM} ${WRKSRC}/multiqc/utils/config.py.orig + +.include Property changes on: head/biology/py-multiqc/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/py-multiqc/distinfo =================================================================== --- head/biology/py-multiqc/distinfo (nonexistent) +++ head/biology/py-multiqc/distinfo (revision 512646) @@ -0,0 +1,3 @@ +TIMESTAMP = 1569116068 +SHA256 (multiqc-1.7.tar.gz) = 02e6a7fac7cd9ed036dcc6c92b8f8bcacbd28983ba6be53afb35e08868bd2d68 +SIZE (multiqc-1.7.tar.gz) = 1168389 Property changes on: head/biology/py-multiqc/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/py-multiqc/files/patch-multiqc_utils_config.py =================================================================== --- head/biology/py-multiqc/files/patch-multiqc_utils_config.py (nonexistent) +++ head/biology/py-multiqc/files/patch-multiqc_utils_config.py (revision 512646) @@ -0,0 +1,41 @@ +--- multiqc/utils/config.py.orig 2019-09-22 13:24:47 UTC ++++ multiqc/utils/config.py +@@ -42,13 +42,13 @@ MULTIQC_DIR = os.path.dirname(os.path.realpath(inspect + # Default MultiQC config + searchp_fn = os.path.join( MULTIQC_DIR, 'utils', 'config_defaults.yaml') + with open(searchp_fn) as f: +- configs = yaml.load(f) ++ configs = yaml.load(f, Loader=yaml.FullLoader) + for c, v in configs.items(): + globals()[c] = v + # Module filename search patterns + searchp_fn = os.path.join( MULTIQC_DIR, 'utils', 'search_patterns.yaml') + with open(searchp_fn) as f: +- sp = yaml.load(f) ++ sp = yaml.load(f, Loader=yaml.FullLoader) + + # Other defaults that can't be set in YAML + data_tmp_dir = '/tmp' # will be overwritten by core script +@@ -118,7 +118,7 @@ def mqc_load_config(yaml_config): + if os.path.isfile(yaml_config): + try: + with open(yaml_config) as f: +- new_config = yaml.load(f) ++ new_config = yaml.load(f, Loader=yaml.FullLoader) + logger.debug("Loading config settings from: {}".format(yaml_config)) + mqc_add_config(new_config, yaml_config) + except (IOError, AttributeError) as e: +@@ -132,11 +132,11 @@ def mqc_load_config(yaml_config): + def mqc_cl_config(cl_config): + for clc_str in cl_config: + try: +- parsed_clc = yaml.load(clc_str) ++ parsed_clc = yaml.load(clc_str, Loader=yaml.FullLoader) + # something:var fails as it needs a space. Fix this (a common mistake) + if isinstance(parsed_clc, str) and ':' in clc_str: + clc_str = ': '.join(clc_str.split(':')) +- parsed_clc = yaml.load(clc_str) ++ parsed_clc = yaml.load(clc_str, Loader=yaml.FullLoader) + assert(isinstance(parsed_clc, dict)) + except yaml.scanner.ScannerError as e: + logger.error("Could not parse command line config: {}\n{}".format(clc_str, e)) Property changes on: head/biology/py-multiqc/files/patch-multiqc_utils_config.py ___________________________________________________________________ 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/py-multiqc/files/patch-scripts_multiqc =================================================================== --- head/biology/py-multiqc/files/patch-scripts_multiqc (nonexistent) +++ head/biology/py-multiqc/files/patch-scripts_multiqc (revision 512646) @@ -0,0 +1,32 @@ +--- scripts/multiqc.orig 2018-12-21 17:29:54 UTC ++++ scripts/multiqc +@@ -6,18 +6,26 @@ + from __future__ import print_function + + import base64 +-import click ++import os ++import sys ++ ++if 'LC_ALL' in os.environ and 'LANG' in os.environ: ++ import click ++else: ++ print('multiqc: LC_ALL and LANG must be set to a UTF-8 character set') ++ print('in your environment in order for the click module to function.') ++ print('E.g. export LC_ALL=en_US.UTF-8 or setenv LC_ALL en_US.UTF-8') ++ sys.exit() ++ + from distutils import version + from distutils.dir_util import copy_tree + import errno + import io + import jinja2 +-import os + import pkg_resources + import re + import shutil + import subprocess +-import sys + import tempfile + import traceback + Property changes on: head/biology/py-multiqc/files/patch-scripts_multiqc ___________________________________________________________________ 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/py-multiqc/pkg-descr =================================================================== --- head/biology/py-multiqc/pkg-descr (nonexistent) +++ head/biology/py-multiqc/pkg-descr (revision 512646) @@ -0,0 +1,5 @@ +MultiQC searches a given directory for analysis logs and compiles an HTML +report. It's a general use tool, perfect for summarising the output from +numerous bioinformatics tools. + +WWW: https://pypi.python.org/pypi/multiqc Property changes on: head/biology/py-multiqc/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