add mtsv recipe

recipes/advntr/meta.yaml

@@ -1,11 +1,12 @@
-{% set version="1.2.0" %}
+{% set version="1.3.0" %}
 
 package:
   name: advntr
   version: {{ version }}
 
 build:
-  number: 0
+  skip: True  # [py==37]
+  number: 1
   script:
     - ./build_advntr_filtering.sh
     - python -m pip install --no-deps --ignore-installed .
@@ -14,7 +15,7 @@ build:
 
 source:
   url: https://github.com/mehrdadbakhtiari/adVNTR/archive/{{ version }}.tar.gz
-  sha256: bb9cbb772687a548dfe5b586b152aeff29bc612062041d1a513ad1d660710b36
+  sha256: 9f36e9c55901f03cef12576623840ad4c07c750077bf11257a9a6a5c54ba558f
 
 requirements:
   build:
@@ -28,21 +29,20 @@ requirements:
     - cython
     - numpy
     - scipy
-    - networkx ==1.11
+    - networkx 1.11
     - matplotlib
   run:
     - python
     - cython
     - {{ pin_compatible('numpy') }}
     - scipy
-    - networkx ==1.11
+    - networkx 1.11
     - joblib
     - scikit-learn
     - biopython
-    - blast
     - muscle
-    - pysam >=0.9.1.4
-    - htslib ==1.3
+    - pysam 0.15.1
+    - htslib 1.9
 
 test:
   commands:

recipes/augustus/build.sh

@@ -12,24 +12,21 @@ export BOOST_LIBRARY_DIR=${PREFIX}/lib
 export CXXFLAGS=" -std=c++11  -DUSE_BOOST -I${BOOST_INCLUDE_DIR} -L${BOOST_LIBRARY_DIR}"
 export LDFLAGS="-L${BOOST_LIBRARY_DIR}"
 
-mkdir -p $PREFIX/bin
-mkdir -p $PREFIX/scripts
-mkdir -p $PREFIX/config
+mkdir -p ${PREFIX}/bin
+mkdir -p ${PREFIX}/scripts
+mkdir -p ${PREFIX}/config
+
 
 ## Make the software
 
-sed -i.bak -e 's/^CC *=/CXX=/' -e 's/\$(CC)/$(CXX)/g' auxprogs/homGeneMapping/src/Makefile
-sed -i.bak -e 's/^CC *=/CXX=/' -e 's/\$(CC)/$(CXX)/g' auxprogs/joingenes/Makefile
-# TODO: don't set CC/CXX here when switching to newer compilers
-CC=gcc
-CXX=g++
 if [ "$(uname)" == Darwin ] ; then
   # SQLITE disabled due to compile issue, see: https://svn.boost.org/trac10/ticket/13501
   make CC="${CC}" CXX="${CXX}" COMPGENPRED=true
 else
   make CC="${CC}" CXX="${CXX}" COMPGENPRED=true SQLITE=true
 fi
 
+
 ## Build Perl
 
 mkdir perl-build
@@ -42,20 +39,25 @@ perl ./Build install --installdirs site
 
 cd ..
 
+
 ## End build perl
 
 mv bin/* $PREFIX/bin/
 mv scripts/* $PREFIX/bin/
 mv config/* $PREFIX/config/
 
-#Add some options to activate
 
-mkdir -p $PREFIX/etc/conda/activate.d/
-echo "export AUGUSTUS_CONFIG_PATH=$PREFIX/config/" > $PREFIX/etc/conda/activate.d/augustus-confdir.sh
-chmod a+x $PREFIX/etc/conda/activate.d/augustus-confdir.sh
+## Set AUGUSTUS variables on env activation
 
-mkdir -p $PREFIX/etc/conda/deactivate.d/
-echo "unset AUGUSTUS_CONFIG_PATH" > $PREFIX/etc/conda/deactivate.d/augustus-confdir.sh
-chmod a+x $PREFIX/etc/conda/deactivate.d/augustus-confdir.sh
+mkdir -p ${PREFIX}/etc/conda/activate.d ${PREFIX}/etc/conda/deactivate.d
+cat <<EOF >> ${PREFIX}/etc/conda/activate.d/augustus.sh
+export AUGUSTUS_CONFIG_PATH=${PREFIX}/config/
+export AUGUSTUS_SCRIPTS_PATH=${PREFIX}/bin/
+export AUGUSTUS_BIN_PATH=${PREFIX}/bin/
+EOF
 
-chmod u+rwx $PREFIX/bin/*
+cat <<EOF >> ${PREFIX}/etc/conda/deactivate.d/augustus.sh
+unset AUGUSTUS_CONFIG_PATH
+unset AUGUSTUS_SCRIPTS_PATH
+unset AUGUSTUS_BIN_PATH
+EOF

recipes/augustus/meta.yaml

@@ -1,127 +1,161 @@
-{% set name = "augustus" %}
-{% set version = "3.3" %}
-{% set sha256 = "b5eb811a4c33a2cc3bbd16355e19d530eeac6d1ac923e59f48d7a79f396234ee" %}
+{% set name = "Augustus" %}
+{% set version = "3.3.2" %}
+{% set sha256 = "d09f972cfd88deb34b19b69878eb8af3bbbe4f1cde1434b69cedc2aa6247a0f2" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
-  url: http://bioinf.uni-greifswald.de/augustus/binaries/old/{{ name }}-{{ version }}.tar.gz
+  url: https://github.com/Gaius-Augustus/{{ name }}/archive/{{ version }}.tar.gz
   sha256: {{ sha256 }}
   patches:
-    - patches/bam2hints.Makefile.patch
-    - patches/filterBam.src.Makefile.patch
-    - patches/filterBam.Makefile.patch
-    - patches/compileSpliceCands.Makefile.patch
+    - patches/bam2hints.makefile.patch
+    - patches/bam2wig.makefile.patch
+    - patches/compileSpliceCands.makefile.patch
+    - patches/filterBam.makefile.patch
+    - patches/filterBam.src.makefile.patch  # [linux]
+    - patches/filterBam.src.makefile.patch.osx  # [osx]
+    - patches/homGeneMapping.src.makefile.patch
+    - patches/joingenes.makefile.patch
+    - patches/utrrnaseq.src.patch
+    - patches/utrrnaseq.patch
+    - patches/src.makefile.patch
 
 build:
-  number: 5
+  number: 0
 
 requirements:
   build:
     - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
   host:
     - zlib
-    - bamtools
+    - bamtools >=2.5
+    - samtools ==0.1.19
+    - htslib
     - gsl
     - lp_solve
-    - perl
-    - perl-module-build
     - boost
     - sqlite
     - suitesparse
     - openblas
+    - perl
+    - perl-module-build
+    - libcblas
   run:
     - zlib
     - bamtools
     - boost
     - gsl
     - lp_solve
+    - biopython
     - perl
     - perl-app-cpanminus
     - perl-module-build
     - perl-yaml
     - perl-dbi
     - perl-scalar-list-utils
+    - perl-file-which
+    - perl-parallel-forkmanager
     - sqlite
     - suitesparse
     - openblas
+    - libcblas
 
 test:
   commands:
     - augustus --version
-    - autoAug.pl --help &>/dev/null
-    - bedgraph2wig.pl --help &>/dev/null
-    - blat2gbrowse.pl --help 2>&1 | grep "convert blat file to gbrowse file" &>/dev/null
-    - blat2hints.pl --help
-    - cegma2gff.pl --help 2>&1 | grep "Could not open CEGMA file --help"
-    - checkParamArchive.pl --help 2>&1 | grep "checkParamArchive.pl param-archive.tar.gz projectDir > utrPossible 2> errors"
-    - cleanDOSfasta.pl --help 2>&1 | grep "Could not open file --help"
+    - aa2nonred.pl --help 2>&1 | grep "aa2nonred.pl" > /dev/null
+    - autoAug.pl --help
+    - autoAugPred.pl --help
+    - autoAugTrain.pl --help 2>&1 | grep "autoAugTrain.pl" > /dev/null
+    - bam2hints --help
+    - bam2wig 2>&1 | grep "bam2wig" > /dev/null
+    - bedgraph2wig.pl
+    - blat2gbrowse.pl --help 2>&1 | grep "blat2gbrowse.pl" > /dev/null
+    - blat2hints.pl
+    - cegma2gff.pl 2>&1 | grep "cegma2gff.pl" > /dev/null
+    - checkParamArchive.pl
+    - cleanDOSfasta.pl
     - clusterAndSplitGenes.pl --help
-    - createAugustusJoblist.pl --help
-    - del_from_prfl.pl --help 2>&1 | grep "Need two arguments"
+    - computeFlankingRegion.pl 2>&1 | grep "computeFlankingRegion.pl" > /dev/null
+    - createAugustusJoblist.pl
+    - del_from_prfl.pl --help 2>&1 | grep "del_from_prfl.pl" > /dev/null
+    - evalCGP.pl
     - eval_dualdecomp.pl --help
-    - evalCGP.pl --help
-    - exonerate2hints.pl --help
-    - echo "hello" | exoniphyDb2hints.pl
-    - echo "hello" | extractTranscriptEnds.pl | grep ">seq1"
-    - filterBam --help 2>&1 | grep "filterBam --in in.bam --out out.bam"
-    - filterGenesIn_mRNAname.pl --help
-    - filterGenesOut_mRNAname.pl --help
-    - filterGenes.pl --help 2>&1 | grep "usage:filterGenes.pl namefile dbfile"
-    - filterInFrameStopCodons.pl --help 2>&1 | grep "Could not open protein file"
-    - filterMaf.pl --help 2>&1 | grep "filter blocks from a MAF alignment that intersect with a given genomic interval"
-    - echo "hello" | filter-ppx.pl | grep "hello"
+    - eval_multi_gtf.pl --help 2>&1 | grep "eval_multi_gtf.pl" > /dev/null
+    - exonerate2hints.pl
+    - filterBam --help 2>&1 | grep "filterBam" > /dev/null
+    - filterGenesIn_mRNAname.pl
+    - filterGenesIn.pl
+    - filterGenesOut_mRNAname.pl
+    - filterGenes.pl
+    - filterInFrameStopCodons.pl
+    - filterMaf.pl --help 2>&1 | grep "filterMaf.pl" > /dev/null
     - filterPSL.pl --help
     - filterShrimp.pl --help
-    - filterSpliceHints.pl --help
-    - gbrowseold2gff3.pl --help 2>&1 | grep "gbrowseold2gff3.pl format convert a GFF file"
-    - gbSmallDNA2gff.pl --help 2>&1 | grep "Could not open genbank input file --help"
-    - getAnnoFasta.pl --help 2>&1 | grep "Makes a fasta file with protein sequences (augustus.aa)"
-    - gff2gbSmallDNA.pl --help 2>&1 | grep "convert GFF file and sequence fasta file to minimal genbank format"
-    - gffGetmRNA.pl --help
-    - gp2othergp.pl --help 2>&1 | grep "t open --help"
-    - gtf2gff.pl --help 2>&1 | grep "gtf2gff.pl format convert a GTF file"
-    - hal2maf_split.pl --help 2>&1 | grep "this script works on top of the "
-    - intron2exex.pl --help | grep "intron2exex.pl make a fasta file with exon-exon sequences"
-    - join_mult_hints.pl --help
-    - joinPeptides.pl --help 2>&1 | grep "joinPeptides.pl in1.fa in2.fa > out.fa"
-    - maf2conswig.pl --help | grep "maf2conswig.pl convert maf alignment format"
-    - makeMatchLists.pl --help  2>&1 | grep "t open --help"
-    - makeUtrTrainingSet.pl --help 2>&1 | grep "./makeUtrTrainingSet.pl -- make a genbank or gff training file with "
-    - maskNregions.pl --help 2>&1 | grep "could not open file --help"
-    - moveParameters.pl --help
-    - msa2prfl.pl --help 2>&1 | grep "Converts a Multiple Sequence Alignment"
-    - new_species.pl --help
-    - optimize_augustus.pl --help
-    - partition_gtf2gb.pl --help 2>&1 | grep "Partition a gtf file into gene clusters"
-    - pasapolyA2hints.pl --help 2>&1 | grep "PASA-Output file in fasta-format"
-    - peptides2alternatives.pl --help 2>&1 | grep "peptides2alternatives.pl peptides.aa augustus-genes.aa"
-    - peptides2hints.pl --help 2>&1 | grep "peptides2hints.pl psl-file gff-file fa-file src pri"
-    - polyA2hints.pl --help 2>&1 | grep "transcript end at position p gives rise to a tts hint"
-    - randomSplit.pl --help
-    - ratewig.pl --help 2>&1 | grep "ratewig /path/to/refseqfile/ /path/to/wigfile"
-    - rmRedundantHints.pl --help 2>&1 | grep "rmRedundantHints.pl list1.hints list2.hints > nonredundant.hints"
-    - runAllSim4.pl --help
-    - samMap.pl --help
-    - scipiogff2gff.pl --help 2>&1 | grep "convert a gff from scipio to a gff file"
-    - simpleFastaHeaders.pl --help 2>&1 | grep "in.fa prefix out.fa mapping.txt"
-    - simplifyFastaHeaders.pl --help 2>&1 | grep "in.fa nameStem out.fa header.map"
-    - splitMfasta.pl --help 2>&1 | grep "Unknown option"
-    - split_wiggle.pl --help
-    - summarizeACGTcontent.pl --help 2>&1 | grep "Couldn"
-    - transMap2hints.pl --help 2>&1 | grep "convert transmap alignments to hints file"
-    - uniquePeptides.pl --help 2>&1 | grep "uniquePeptides.pl in.fa prefix > out.fa"
-    - utrgff2gbrowse.pl --help
+    - filterSpliceHints.pl
+    - findGffNamesInFasta.pl --help 2>&1 | grep "file" > /dev/null
+    - gbrowseold2gff3.pl --help 2>&1 | grep "gbrowseold2gff3.pl" > /dev/null
+    - gbSmallDNA2gff.pl 2>&1 | grep "gbSmallDNA2gff.pl" > /dev/null
+    - getAnnoFasta.pl
+    - getLinesMatching.pl 2>&1 | grep "getLinesMatching.pl" > /dev/null
+    - gff2gbSmallDNA.pl 2>&1 | grep "gff2gbSmallDNA.pl" > /dev/null
+    - gffGetmRNA.pl
+    - gp2othergp.pl --help 2>&1 | grep "gp2othergp.pl" > /dev/null
+    - gtf2aa.pl 2>&1 | grep "gtf2aa.pl" > /dev/null
+    - gtf2bed.pl --help 2>&1 | grep "gtf2bed.pl" > /dev/null
+    - gtf2gff.pl --help 2>&1 | grep "gtf2gff.pl" > /dev/null
+    - gth2gtf.pl 2>&1 | grep "gth2gtf.pl" > /dev/null
+    - hal2maf_split.pl --help 2>&1 | grep "hal2maf_split.pl" > /dev/null
+    - homGeneMapping --help 2>&1 | grep "homGeneMapping" > /dev/null
+    - intron2exex.pl --help 2>&1 | grep "intron2exex.pl" > /dev/null
+    - join_mult_hints.pl --help 2>&1 | grep "join_mult_hints.pl" > /dev/null
+    - joingenes --help 2>&1 | grep "joingenes" > /dev/null
+    - joinPeptides.pl 2>&1 | grep "joinPeptides.pl" > /dev/null
+    - maf2conswig.pl --help 2>&1 | grep "maf2conswig.pl" > /dev/null
+    - makeMatchLists.pl --help 2>&1 | grep "help" > /dev/null
+    - makeUtrTrainingSet.pl 2>&1 | grep "makeUtrTrainingSet.pl" > /dev/null
+    - maskNregions.pl
+    - moveParameters.pl
+    - msa2prfl.pl --help
+    - new_species.pl 
+    - optimize_augustus.pl
+    - opt_init_and_term_probs.pl 2>&1 | grep "open" > /dev/null
+    - parseSim4Output.pl 2>&1 | grep "parseSim4Output.pl" > /dev/null
+    - partition_gtf2gb.pl --help 2>&1 | grep "parition_gtf2gb.pl" > /dev/null
+    - pasapolyA2hints.pl 2>&1 | grep "pasapolyA2hints.pl" > /dev/null
+    - peptides2alternatives.pl 2>&1 | grep "peptides2alternatives.pl" > /dev/null
+    - peptides2hints.pl 2>&1 | grep "peptides2hints.pl" > /dev/null
+    - polyA2hints.pl
+    - pslMap.pl 2>&1 | grep "pslMap.pl" > /dev/null
+    - randomSplit.pl
+    - ratewig.pl
+    - rmRedundantHints.pl 2>&1 | grep "rmRedundantHints.pl" > /dev/null
+    - runAllSim4.pl --help 2>&1 | grep "runAllSim4.pl" > /dev/null
+    - samMap.pl
+    - scipiogff2gff.pl 2>&1 | grep "scipiogff2gff.pl" > /dev/null
+    - setStopCodonFreqs.pl 2>&1 | grep "setStopCodonFreqs.pl" > /dev/null
+    - simpleFastaHeaders.pl 2>&1 | grep "simpleFastaHeaders.pl" > /dev/null
+    - simplifyFastaHeaders.pl 2>&1 | grep "simplifyFastaHeaders.pl" > /dev/null
+    - splitMfasta.pl
+    - split_wiggle.pl
+    - summarizeACGTcontent.pl 2>&1 | grep "summarizeACGTcontent.pl" > /dev/null
+    - transMap2hints.pl
+    - uniquePeptides.pl 2>&1 | grep "uniquePeptides.pl" > /dev/null
+    - utrgff2gbrowse.pl --help 2>&1 | grep "utrgff2gbrowse.pl" > /dev/null
+    - weedMaf.pl --help 2>&1 | grep "weedMaf.pl" > /dev/null
     - wigchoose.pl --help
-    - writeResultsPage.pl --help 2>&1 | grep "writeResultsPage ID species-name db-file grails-out www-out AugustusConfigPath AugustusScriptsPath final-flag"
-    - yaml2gff.1.4.pl --help 2>&1 | grep "< scipio.yaml > scipio.gff"
+    - writeResultsPage.pl
+    - yaml2gff.1.4.pl --help 2>&1 | grep "yaml2gff.pl" > /dev/null
+    - getAnnoFastaFromJoingenes.py --help
 
 about:
   home: http://bioinf.uni-greifswald.de/augustus/
-  license: MIT
-  license_family: MIT
+  license: Artistic Licence
+  license_family: Other
+  license_file: "src/LICENCE.TXT"
   summary: 'AUGUSTUS is a gene prediction program for eukaryotes written by Mario
     Stanke and Oliver Keller. It can be used as an ab initio program, which means
     it bases its prediction purely on the sequence. AUGUSTUS may also incorporate
@@ -132,4 +166,4 @@ extra:
   identifiers:
     - biotools:augustus
     - doi:10.1093/bioinformatics/btr010
-  notes: Builds with sqlite support are currently only available on Linux due to compile issues with macOS
+  notes: "Builds with sqlite support are currently only available on Linux due to compile issues with macOS."