Merge remote-tracking branch 'origin/bioconda-import-branch'

research-software-ecosystem · Apr 14, 2024 · e6e2f67 · e6e2f67
2 parents c340b50 + d292ff8
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diff --git a/data/biolib/bioconda_biolib.yaml b/data/biolib/bioconda_biolib.yaml
@@ -6,4 +6,4 @@ license: MIT
 license_file: LICENSE
 name: pybiolib
 summary: BioLib Python Client
-version: 1.1.1942
+version: 1.1.1971
diff --git a/data/cutadapt/bioconda_cutadapt.yaml b/data/cutadapt/bioconda_cutadapt.yaml
@@ -10,4 +10,4 @@ license_family: MIT
 license_file: LICENSE
 name: cutadapt
 summary: Trim adapters from high-throughput sequencing reads
-version: 4.7
+version: 4.8
diff --git a/data/genomad/bioconda_genomad.yaml b/data/genomad/bioconda_genomad.yaml
@@ -9,4 +9,4 @@ license_family: BSD
 license_file: LICENSE
 name: genomad
 summary: Identification of mobile genetic elements
-version: 1.7.6
+version: 1.8.0
diff --git a/data/getorganelle/bioconda_getorganelle.yaml b/data/getorganelle/bioconda_getorganelle.yaml
@@ -0,0 +1,15 @@
+biotools_id: getorganelle
+dev_url: https://github.com/Kinggerm/GetOrganelle
+doc_url: https://github.com/Kinggerm/GetOrganelle/wiki
+home: https://github.com/Kinggerm/GetOrganelle
+identifiers:
+- doi:10.1186/s13059-020-02154-5
+- biotools:getorganelle
+- usegalaxy-eu:get_organelle_from_reads
+- usegalaxy-eu:get_annotated_regions_from_gb
+license: GPL-3.0-or-later
+license_family: GPL3
+license_file: LICENSE
+name: getorganelle
+summary: Get organelle genomes from genome skimming data
+version: 1.7.7.1
diff --git a/data/gffutils/bioconda_gffutils.yaml b/data/gffutils/bioconda_gffutils.yaml
@@ -9,4 +9,4 @@ license_family: MIT
 license_file: LICENSE
 name: gffutils
 summary: Work with GFF and GTF files in a flexible database framework
-version: '0.12'
+version: '0.13'
diff --git a/data/kmc/bioconda_kmc.yaml b/data/kmc/bioconda_kmc.yaml
@@ -1,19 +1,19 @@
 biotools_id: kmc
-description: 'K-mer Counter is a utility designed for counting k-mers (sequences
+description: 'KMC is a utility designed for counting k-mers (sequences
 
-  of consecutive k symbols) in a set of reads from genome sequencing
-
-  projects.
+  of consecutive k symbols) in a set of DNA sequences. KMC tools allow performing
+  various operations on k-mers sets.
 
   '
-home: http://sun.aei.polsl.pl/kmc/
+dev_url: https://github.com/refresh-bio/kmc
+home: https://github.com/refresh-bio/kmc
 identifiers:
-- biotools:KMC
+- biotools:kmc
 - doi:10.1093/bioinformatics/btx304
-license: GPL3
+license: GPL-3
 license_family: GPL3
-license_file: /gpl-3.0.txt
+license_file: gpl-3.0.txt
 name: kmc
 summary: Tools for efficient k-mer counting and filtering of reads based on k-mer
-  content
-version: 3.1.2rc1
+  content.
+version: 3.2.4
diff --git a/data/ntedit/bioconda_ntedit.yaml b/data/ntedit/bioconda_ntedit.yaml
@@ -0,0 +1,14 @@
+biotools_id: ntedit
+dev_url: https://github.com/bcgsc/ntEdit
+doc_url: https://github.com/bcgsc/ntEdit/blob/master/README.md
+home: https://github.com/bcgsc/ntEdit
+identifiers:
+- doi:10.1093/bioinformatics/btz400
+- biotools:ntEdit
+license: GPL-3.0-or-later
+license_family: GPL3
+license_file: LICENSE
+name: ntedit
+summary: Ultrafast, lightweight, scalable genome assembly polishing, and SNV detection
+  & annotation
+version: 2.0.1
diff --git a/data/oakvar/bioconda_oakvar.yaml b/data/oakvar/bioconda_oakvar.yaml
@@ -9,4 +9,4 @@ license_family: AGPL
 license_file: LICENSE
 name: oakvar
 summary: OakVar - Genomic Variant Analysis Platform
-version: 2.9.92
+version: 2.9.96
diff --git a/data/prosampler/bioconda_prosampler.yaml b/data/prosampler/bioconda_prosampler.yaml
@@ -5,4 +5,4 @@ identifiers:
 license: GPLv3
 name: prosampler
 summary: An ultra-fast motif finding program in large ChIP-seq datasets.
-version: 1.0
+version: 1.5
diff --git a/data/pybedtools/bioconda_pybedtools.yaml b/data/pybedtools/bioconda_pybedtools.yaml
@@ -1,8 +1,12 @@
 biotools_id: pybedtools
+dev_url: https://github.com/daler/pybedtools
+doc_url: https://daler.github.io/pybedtools
 home: https://github.com/daler/pybedtools
 identifiers:
 - biotools:pybedtools
 license: MIT
+license_family: MIT
+license_file: LICENSE.txt
 name: pybedtools
 summary: Wraps BEDTools for use in Python and adds many additional features.
-version: 0.9.1
+version: 0.10.0
diff --git a/data/pymzml/bioconda_pymzml.yaml b/data/pymzml/bioconda_pymzml.yaml
@@ -6,4 +6,4 @@ license: MIT
 license_file: LICENSE.txt
 name: pymzml
 summary: high-throughput mzML parsing
-version: 2.5.6
+version: 2.5.9
diff --git a/data/snakemake/bioconda_snakemake.yaml b/data/snakemake/bioconda_snakemake.yaml
@@ -11,4 +11,4 @@ identifiers:
 license: MIT
 name: snakemake
 summary: A popular workflow management system aiming at full in-silico reproducibility.
-version: 8.10.6
+version: 8.10.7
diff --git a/data/sourmash/bioconda_sourmash.yaml b/data/sourmash/bioconda_sourmash.yaml
@@ -11,4 +11,4 @@ license_family: BSD
 license_file: LICENSE
 name: sourmash
 summary: Compute and compare MinHash signatures for DNA data sets.
-version: 4.8.7
+version: 4.8.8
diff --git a/data/vsearch/bioconda_vsearch.yaml b/data/vsearch/bioconda_vsearch.yaml
@@ -8,4 +8,4 @@ license_family: GPL3
 license_file: LICENSE.txt
 name: vsearch
 summary: A versatile open source tool for metagenomics (USEARCH alternative)
-version: 2.27.0
+version: 2.27.1