research-software-ecosystem · bgruening · Jan 27, 2020 · Jan 27, 2020
diff --git a/data/bam2fasta/bioconda_bam2fasta.yaml b/data/bam2fasta/bioconda_bam2fasta.yaml
@@ -0,0 +1,8 @@
+dev_url: https://github.com/czbiohub/bam2fasta
+home: https://github.com/czbiohub/bam2fasta
+license: MIT License
+license_family: MIT
+license_file: LICENSE
+name: bam2fasta
+summary: 'bam2fasta: cli tool to convert bam to fastas'
+version: 1.0.1
diff --git a/data/bold-identification/bioconda_bold-identification.yaml b/data/bold-identification/bioconda_bold-identification.yaml
@@ -0,0 +1,8 @@
+home: https://github.com/linzhi2013/bold_identification
+license: GNU General Public v3 or later (GPLv3+)
+license_family: GPL3
+license_file: LICENSE
+name: bold-identification
+summary: A tool for taxonomic assignment for given sequences using the BOLD database
+  (http://www.boldsystems.org/index.php)
+version: 0.0.25
diff --git a/data/chorus2/bioconda_chorus2.yaml b/data/chorus2/bioconda_chorus2.yaml
@@ -0,0 +1,8 @@
+dev_url: https://github.com/zhangtaolab/Chorus2
+doc_url: https://chorus2.readthedocs.io/en/dev/
+home: https://github.com/zhangtaolab/Chorus2
+license: MIT license
+name: chorus2
+summary: A pipeline to select oligonucleotides for fluorescence in situ hbridization
+  (Oligo-FISH).
+version: 2.0
diff --git a/data/extract_fasta_seq/bioconda_extract_fasta_seq.yaml b/data/extract_fasta_seq/bioconda_extract_fasta_seq.yaml
@@ -0,0 +1,7 @@
+home: https://github.com/linzhi2013/extract_fasta_seq
+license: GNU General Public v3 or later (GPLv3+)
+license_family: GPL3
+license_file: LICENSE
+name: extract_fasta_seq
+summary: To extract specific fasta sequences from a fasta file.
+version: 0.0.1
diff --git a/data/faqcs/bioconda_faqcs.yaml b/data/faqcs/bioconda_faqcs.yaml
@@ -0,0 +1,6 @@
+home: https://github.com/LANL-Bioinformatics/FaQCs
+license: BSD 3-Clause
+license_file: LICENSE
+name: faqcs
+summary: Quality Control of Next Generation Sequencing Data.
+version: 2.09
diff --git a/data/gem_mapper/bioconda_gem_mapper.yaml b/data/gem_mapper/bioconda_gem_mapper.yaml
@@ -0,0 +1,6 @@
+home: https://github.com/smarco/gem3-mapper
+license: GPL-3.0
+license_file: LICENSE
+name: gem3-mapper
+summary: The GEM read mapper (v3).
+version: 3.6.1
diff --git a/data/ispcr/bioconda_ispcr.yaml b/data/ispcr/bioconda_ispcr.yaml
@@ -0,0 +1,6 @@
+home: https://users.soe.ucsc.edu/~kent/
+license: License is hereby granted for personal, academic, and non-profit use.
+license_file: README
+name: ispcr
+summary: In silico PCR
+version: 33
diff --git a/data/ivar/bioconda_ivar.yaml b/data/ivar/bioconda_ivar.yaml
@@ -0,0 +1,8 @@
+dev_url: https://github.com/andersen-lab/ivar
+home: https://andersen-lab.github.io/ivar/html/
+license: GPL-3.0
+license_file: LICENSE
+name: ivar
+summary: iVar is a computational package that contains functions broadly useful for
+  viral amplicon-based sequencing.
+version: 1.0.1
diff --git a/data/krakenhll/bioconda_krakenhll.yaml b/data/krakenhll/bioconda_krakenhll.yaml
@@ -0,0 +1,6 @@
+home: https://github.com/fbreitwieser/krakenuniq
+license: GPLv3
+license_file: LICENSE
+name: krakenuniq
+summary: Metagenomics classifier with unique k-mer counting for more specific results
+version: 0.5.8
diff --git a/data/ksw/bioconda_ksw.yaml b/data/ksw/bioconda_ksw.yaml
@@ -0,0 +1,6 @@
+home: https://github.com/nh13/ksw
+license: MIT
+license_file: LICENSE
+name: ksw
+summary: 'Ksw: (interactive) smith-waterman in C'
+version: 0.2.1
diff --git a/data/magicblast/bioconda_magicblast.yaml b/data/magicblast/bioconda_magicblast.yaml
@@ -0,0 +1,17 @@
+description: "Magic-BLAST is a tool for mapping large next-generation RNA or DNA \n\
+  sequencing runs against a whole genome or transcriptome. Each alignment\noptimizes\
+  \ a composite score, taking into account simultaneously the two\nreads of a pair,\
+  \ and in case of RNA-seq, locating the candidate introns\nand adding up the score\
+  \ of all exons. This is very different from other\nversions of BLAST, where each\
+  \ exon is scored as a separate hit and\nread-pairing is ignored.\n\nMagic-BLAST\
+  \ incorporates within the NCBI BLAST code framework ideas \ndeveloped in the NCBI\
+  \ Magic pipeline, in particular hit extensions by local \nwalk and jump (http://www.ncbi.nlm.nih.gov/pubmed/26109056),\
+  \ and \nrecursive clipping of mismatches near the edges of the reads, which avoids\n\
+  accumulating artefactual mismatches near splice sites and is needed to\ndistinguish\
+  \ short indels from substitutions near the edges.\n\nMore details about the algorithm\
+  \ and comparison with other similar tools\nare presented here:\nhttps://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2996-x.\n"
+home: https://ncbi.github.io/magicblast/
+license: Public Domain
+name: magicblast
+summary: NCBI BLAST next generation read mapper
+version: 1.5.0
diff --git a/data/malt/bioconda_malt.yaml b/data/malt/bioconda_malt.yaml
@@ -0,0 +1,5 @@
+home: http://ab.inf.uni-tuebingen.de/software/malt/
+license: GPLv3
+name: malt
+summary: A tool for mapping metagenomic data
+version: 0.41
diff --git a/data/malva/bioconda_malva.yaml b/data/malva/bioconda_malva.yaml
@@ -0,0 +1,5 @@
+home: https://algolab.github.io/malva/
+license: GPL-3.0-or-later
+name: malva
+summary: genotyping by Mapping-free ALternate-allele detection of known VAriants
+version: 1.1.1
diff --git a/data/manta9235/bioconda_manta9235.yaml b/data/manta9235/bioconda_manta9235.yaml
@@ -0,0 +1,5 @@
+home: https://github.com/Illumina/manta
+license: GPLv3
+name: manta
+summary: Structural variant and indel caller for mapped sequencing data
+version: 1.6.0
diff --git a/data/mgkit/bioconda_mgkit.yaml b/data/mgkit/bioconda_mgkit.yaml
@@ -0,0 +1,6 @@
+home: https://github.com/frubino/mgkit
+license: GNU General Public License v2 or later (GPLv2+)
+license_family: GPL2
+name: mgkit
+summary: Metagenomics Framework
+version: 0.4.1
diff --git a/data/miniax/bioconda_miniax.yaml b/data/miniax/bioconda_miniax.yaml
@@ -0,0 +1,7 @@
+home: https://github.com/GATB/minia
+license: file
+license_file: LICENSE
+name: minia
+summary: Minia is a short-read assembler based on a de Bruijn graph, capable of assembling
+  a human genome on a desktop computer in a day.
+version: 3.2.1
diff --git a/data/mirtop/bioconda_mirtop.yaml b/data/mirtop/bioconda_mirtop.yaml
@@ -0,0 +1,6 @@
+home: http://github.com/mirtop/mirtop
+license: MIT License
+license_family: MIT
+name: mirtop
+summary: Small RNA-seq annotation
+version: 0.4.23
diff --git a/data/mutmap/bioconda_mutmap.yaml b/data/mutmap/bioconda_mutmap.yaml
@@ -0,0 +1,6 @@
+home: https://github.com/YuSugihara/MutMap
+license: GPL-3.0-or-later
+license_family: GPL
+name: mutmap
+summary: 'MutMap: pipeline to identify causative mutations responsible for a phenotype'
+version: 2.1.3
diff --git a/data/ngmerge/bioconda_ngmerge.yaml b/data/ngmerge/bioconda_ngmerge.yaml
@@ -0,0 +1,6 @@
+home: https://github.com/harvardinformatics/NGmerge
+license: MIT
+license_file: LICENSE
+name: ngmerge
+summary: Merging paired-end reads and removing sequencing adapters.
+version: 0.3
diff --git a/data/pgcgap/bioconda_pgcgap.yaml b/data/pgcgap/bioconda_pgcgap.yaml
@@ -0,0 +1,8 @@
+dev_url: https://github.com/liaochenlanruo/pgcgap/tree/master
+home: https://github.com/liaochenlanruo/pgcgap/blob/master/README.md
+license: GPLv3
+license_family: GPL
+license_file: LICENSE
+name: pgcgap
+summary: A prokaryotic genomics and comparative genomics analysis pipeline
+version: 1.0.9
diff --git a/data/phame/bioconda_phame.yaml b/data/phame/bioconda_phame.yaml
@@ -0,0 +1,6 @@
+home: https://github.com/LANL-Bioinformatics/PhaME
+license: GPLV2
+name: phame
+summary: A tool to derive SNP matrices and phylogenetic tree from raw reads, contigs,
+  and full genomes.
+version: 1.0.3
diff --git a/data/phylocsf/bioconda_phylocsf.yaml b/data/phylocsf/bioconda_phylocsf.yaml
@@ -0,0 +1,7 @@
+home: https://github.com/mlin/PhyloCSF/wiki
+license: AGPL-3.0
+license_file: LICENSE
+name: phylocsf
+summary: Phylogenetic analysis of multi-species genome sequence alignments to identify
+  conserved protein-coding regions
+version: 1.0.1
diff --git a/data/pirate/bioconda_pirate.yaml b/data/pirate/bioconda_pirate.yaml
@@ -0,0 +1,7 @@
+home: https://github.com/SionBayliss/PIRATE
+license: GPL3
+license_family: GPL
+license_file: LICENSE
+name: pirate
+summary: Pangenome analysis and threshold evaluation toolbox
+version: 1.0.3
diff --git a/data/piret/bioconda_piret.yaml b/data/piret/bioconda_piret.yaml
@@ -0,0 +1,5 @@
+home: https://github.com/mshakya/PyPiReT
+license: GPLV2
+name: piret
+summary: A tool for conducting RNA seq analysis.
+version: 0.3.4
diff --git a/data/popera/bioconda_popera.yaml b/data/popera/bioconda_popera.yaml
@@ -0,0 +1,7 @@
+dev_url: https://github.com/forrestzhang/Popera
+home: https://github.com/forrestzhang/Popera
+license: MIT
+license_file: LICENSE
+name: popera
+summary: A software for DNase I hypersensitive sites identification.
+version: 1.0.3
diff --git a/data/qtlseq/bioconda_qtlseq.yaml b/data/qtlseq/bioconda_qtlseq.yaml
@@ -0,0 +1,6 @@
+home: https://github.com/YuSugihara/QTL-seq
+license: GPL-3.0-or-later
+license_family: GPL
+name: qtlseq
+summary: 'QTL-seq: pipeline to identify causative mutations responsible for a phenotype'
+version: 2.0.7
diff --git a/data/referenceseeker/bioconda_referenceseeker.yaml b/data/referenceseeker/bioconda_referenceseeker.yaml
@@ -0,0 +1,8 @@
+dev_url: https://github.com/oschwengers/referenceseeker
+home: https://github.com/oschwengers/referenceseeker
+license: GPLv3
+license_family: GPL
+license_file: LICENSE
+name: referenceseeker
+summary: Rapid determination of appropriate reference genomes.
+version: '1.4'
diff --git a/data/sepp-refgg138/bioconda_sepp-refgg138.yaml b/data/sepp-refgg138/bioconda_sepp-refgg138.yaml
@@ -0,0 +1,7 @@
+home: https://github.com/smirarab/sepp-refs
+license: GPLv3
+license_family: GPL3
+license_file: LICENSE
+name: sepp-refgg138
+summary: SATe-enabled phylogenetic placement
+version: 4.3.6
diff --git a/data/sepp-refsilva128/bioconda_sepp-refsilva128.yaml b/data/sepp-refsilva128/bioconda_sepp-refsilva128.yaml
@@ -0,0 +1,7 @@
+home: https://github.com/smirarab/sepp-refs
+license: GPLv3
+license_family: GPL3
+license_file: LICENSE
+name: sepp-refsilva128
+summary: SATe-enabled phylogenetic placement
+version: 4.3.6
diff --git a/data/sepp/bioconda_sepp.yaml b/data/sepp/bioconda_sepp.yaml
@@ -0,0 +1,7 @@
+home: https://github.com/smirarab/sepp
+license: GPLv3
+license_family: GPL3
+license_file: LICENSE
+name: sepp
+summary: SATe-enabled phylogenetic placement
+version: 4.3.10
diff --git a/data/shark/bioconda_shark.yaml b/data/shark/bioconda_shark.yaml
@@ -0,0 +1,6 @@
+home: https://algolab.github.io/shark/
+license: GPL-3.0-or-later
+license_file: LICENSE
+name: shark
+summary: Mapping-free filtering of useless RNA-Seq reads
+version: 1.0.0
diff --git a/data/slimm/bioconda_slimm.yaml b/data/slimm/bioconda_slimm.yaml
@@ -0,0 +1,5 @@
+home: https://github.com/seqan/slimm/blob/master/README.md
+license: https://github.com/seqan/slimm/blob/master/LICENSE
+name: slimm
+summary: SLIMM - Species Level Identification of Microbes from Metagenomes
+version: 0.3.4
diff --git a/data/super_distance/bioconda_super_distance.yaml b/data/super_distance/bioconda_super_distance.yaml
@@ -0,0 +1,6 @@
+home: https://github.com/quadram-institute-bioscience/super_distance
+license: GPLv3
+license_file: LICENSE
+name: super_distance
+summary: Supertree method with distances
+version: 1.1.0
diff --git a/data/taxonomy_ranks/bioconda_taxonomy_ranks.yaml b/data/taxonomy_ranks/bioconda_taxonomy_ranks.yaml
@@ -0,0 +1,8 @@
+home: https://github.com/linzhi2013/taxonomy_ranks
+license: GNU General Public v3 or later (GPLv3+)
+license_family: GPL3
+license_file: LICENSE
+name: taxonomy_ranks
+summary: To get taxonomy ranks information for taxid, species name, or higher ranks
+  (e.g., genus, family) with ETE3 from NCBI Taxonomy database.
+version: 0.0.7
diff --git a/data/thesias/bioconda_thesias.yaml b/data/thesias/bioconda_thesias.yaml
@@ -0,0 +1,5 @@
+home: https://github.com/daissi/thesias
+license: GPL-3+
+name: thesias
+summary: Testing Haplotype Effects In Association Studies
+version: 3.1.1
diff --git a/data/wham6216/bioconda_wham6216.yaml b/data/wham6216/bioconda_wham6216.yaml
@@ -0,0 +1,6 @@
+home: https://github.com/zeeev/wham
+license: MIT
+license_family: MIT
+name: wham
+summary: Structural variant detection and association testing
+version: 1.8.0.1.2017.05.03
diff --git a/data/womtool/bioconda_womtool.yaml b/data/womtool/bioconda_womtool.yaml
@@ -0,0 +1,7 @@
+home: https://cromwell.readthedocs.io/en/develop/WOMtool/
+license: BSD-3-Clause
+license_family: BSD
+license_file: LICENSE.txt
+name: womtool
+summary: Command line utilities for interacting with WDL
+version: 48
diff --git a/data/xhmm/bioconda_xhmm.yaml b/data/xhmm/bioconda_xhmm.yaml
@@ -0,0 +1,5 @@
+home: http://atgu.mgh.harvard.edu/xhmm/index.shtml
+license: GPL3
+name: xhmm
+summary: XHMM (eXome-Hidden Markov Model).
+version: 0.0.0.2016_01_04.cc14e52