diff --git a/Program_Licenses.md b/Program_Licenses.md index 83bf16e01..bda48be96 100644 --- a/Program_Licenses.md +++ b/Program_Licenses.md @@ -18,7 +18,7 @@ The licenses of the open-source software that is contained in these Docker image | Bakta | GNU GPLv3 | https://github.com/oschwengers/bakta/blob/main/LICENSE | | Bandage | GNU GPLv3 | https://github.com/rrwick/Bandage?tab=GPL-3.0-1-ov-file#readme | | BBTools | non-standard - see `licence.txt` and `legal.txt` that is included in docker image under `/bbmap/docs/`; Also on sourceforge repo for BBTools | https://jgi.doe.gov/disclaimer/ | -| bcftools | MIT or **GNU GPLv3** (depends on how bcftools was compiled, I believe GNU GPLv3 applies here) | https://github.com/samtools/bcftools/blob/develop/LICENSE | +| bcftools | MIT & **GNU GPLv3** | https://github.com/samtools/bcftools/blob/develop/LICENSE | | bedtools | MIT | https://github.com/arq5x/bedtools2/blob/master/LICENSE | | blast+ | Public Domain | https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/scripts/projects/blast/LICENSE | | bowtie2 | GNU GPLv3 | https://github.com/BenLangmead/bowtie2/blob/master/LICENSE | diff --git a/README.md b/README.md index 16b6056e5..bcd0eba9f 100644 --- a/README.md +++ b/README.md @@ -119,7 +119,7 @@ To learn more about the docker pull rate limits and the open source software pro | [bakta](https://hub.docker.com/r/staphb/bakta)
[![docker pulls](https://badgen.net/docker/pulls/staphb/bakta)](https://hub.docker.com/r/staphb/bakta) | | https://github.com/oschwengers/bakta | | [bandage](https://hub.docker.com/r/staphb/bandage)
[![docker pulls](https://badgen.net/docker/pulls/staphb/bandage)](https://hub.docker.com/r/staphb/bandage) | | https://rrwick.github.io/Bandage/ | | [BBTools](https://hub.docker.com/r/staphb/bbtools/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/bbtools)](https://hub.docker.com/r/staphb/bbtools) | | https://jgi.doe.gov/data-and-tools/bbtools/ | -| [bcftools](https://hub.docker.com/r/staphb/bcftools/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/bcftools)](https://hub.docker.com/r/staphb/bcftools) | | https://github.com/samtools/bcftools | +| [bcftools](https://hub.docker.com/r/staphb/bcftools/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/bcftools)](https://hub.docker.com/r/staphb/bcftools) | | https://github.com/samtools/bcftools | | [bedtools](https://hub.docker.com/r/staphb/bedtools/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/bedtools)](https://hub.docker.com/r/staphb/bedtools) | | https://bedtools.readthedocs.io/en/latest/
https://github.com/arq5x/bedtools2 | | [berrywood-report-env](https://hub.docker.com/r/staphb/berrywood-report-env/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/berrywood-report-env)](https://hub.docker.com/r/staphb/berrywood-report-env) | | none | | [blast+](https://hub.docker.com/r/staphb/blast/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/blast)](https://hub.docker.com/r/staphb/blast) | | https://www.ncbi.nlm.nih.gov/books/NBK279690/ | @@ -172,7 +172,7 @@ To learn more about the docker pull rate limits and the open source software pro | [heatcluster](https://hub.docker.com/r/staphb/heatcluster)
[![docker pulls](https://badgen.net/docker/pulls/staphb/heatcluster)](https://hub.docker.com/r/staphb/heatcluster) | | https://github.com/DrB-S/heatcluster/tree/main | | [hmmer](https://hub.docker.com/r/staphb/hmmer)
[![docker pulls](https://badgen.net/docker/pulls/staphb/hmmer)](https://hub.docker.com/r/staphb/hmmer) | | http://hmmer.org/ | | [homopolish](https://hub.docker.com/r/staphb/homopolish)
[![docker pulls](https://badgen.net/docker/pulls/staphb/homopolish)](https://hub.docker.com/r/staphb/homopolish) | | https://github.com/ythuang0522/homopolish/ | -| [htslib](https://hub.docker.com/r/staphb/htslib)
[![docker pulls](https://badgen.net/docker/pulls/staphb/htslib)](https://hub.docker.com/r/staphb/htslib) | | https://www.htslib.org/ | +| [htslib](https://hub.docker.com/r/staphb/htslib)
[![docker pulls](https://badgen.net/docker/pulls/staphb/htslib)](https://hub.docker.com/r/staphb/htslib) | | https://www.htslib.org/ | | [iqtree](https://hub.docker.com/r/staphb/iqtree/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/iqtree)](https://hub.docker.com/r/staphb/iqtree) | | http://www.iqtree.org/ | | [iqtree2](https://hub.docker.com/r/staphb/iqtree2/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/iqtree2)](https://hub.docker.com/r/staphb/iqtree2) | | http://www.iqtree.org/ | | [IPA](https://hub.docker.com/r/staphb/pbipa)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pbipa)](https://hub.docker.com/r/staphb/pbipa) | | https://github.com/PacificBiosciences/pbipa | @@ -255,7 +255,7 @@ To learn more about the docker pull rate limits and the open source software pro | [Roary](https://hub.docker.com/r/staphb/roary/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/roary)](https://hub.docker.com/r/staphb/roary) | | https://github.com/sanger-pathogens/Roary | | [SalmID](https://hub.docker.com/r/staphb/salmid)
[![docker pulls](https://badgen.net/docker/pulls/staphb/salmid)](https://hub.docker.com/r/staphb/salmid) | | https://github.com/hcdenbakker/SalmID | | [samclip](https://hub.docker.com/r/staphb/samclip)
[![docker pulls](https://badgen.net/docker/pulls/staphb/samclip)](https://hub.docker.com/r/staphb/samclip) | | https://github.com/tseemann/samclip | -| [Samtools](https://hub.docker.com/r/staphb/samtools)
[![docker pulls](https://badgen.net/docker/pulls/staphb/samtools)](https://hub.docker.com/r/staphb/samtools) | | https://github.com/samtools/samtools | +| [Samtools](https://hub.docker.com/r/staphb/samtools)
[![docker pulls](https://badgen.net/docker/pulls/staphb/samtools)](https://hub.docker.com/r/staphb/samtools) | | https://github.com/samtools/samtools | | [SeqKit](https://hub.docker.com/r/staphb/SeqKit)
[![docker pulls](https://badgen.net/docker/pulls/staphb/seqkit)](https://hub.docker.com/r/staphb/seqkit) | | https://github.com/shenwei356/seqkit | | [SeqSero](https://hub.docker.com/r/staphb/seqsero/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/seqsero)](https://hub.docker.com/r/staphb/seqsero) | | https://github.com/denglab/SeqSero | | [SeqSero2](https://hub.docker.com/r/staphb/seqsero2/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/seqsero2)](https://hub.docker.com/r/staphb/seqsero2) | | https://github.com/denglab/SeqSero2/ | diff --git a/bcftools/1.20.c/README.md b/bcftools/1.20.c/README.md index d1376bb34..473a0f659 100644 --- a/bcftools/1.20.c/README.md +++ b/bcftools/1.20.c/README.md @@ -1,8 +1,20 @@ # bcftools container -Main tool: +Main tool: [bcftools](https://github.com/samtools/bcftools) -* [bcftools](https://github.com/samtools/bcftools) +Code repository: https://github.com/samtools/bcftools + +Basic information on how to use this tool: +- executable: bcftools +- help: --help +- version: --version +- description: BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF. + +Additional information: + +This container includes bcftools v1.20 compiled with **libdeflate** for a better cloud performance. Also, "polysomy" and plugins are enabled in this image. + +Full documentation: https://samtools.github.io/bcftools/howtos/index.html ## Example Usage @@ -10,4 +22,4 @@ Main tool: bcftools mpileup -A -d 200 -B -Q 0 -f {reference_genome} {bam} | bcftools call -mv -Ov -o bcftools_variants/{sample}.vcf ``` -Better documentation can be found at [https://www.htslib.org/doc/bcftools.html](https://www.htslib.org/doc/bcftools.html) + diff --git a/htslib/1.20.c/README.md b/htslib/1.20.c/README.md index 7d03b6333..a165c9212 100644 --- a/htslib/1.20.c/README.md +++ b/htslib/1.20.c/README.md @@ -1,14 +1,25 @@ # htslib container -Main tool: +Main tool: [htslib](https://www.htslib.org/) -* [https://www.htslib.org/](https://www.htslib.org/) -* [GitHub](https://github.com/samtools/htslib) +Code repository: https://github.com/samtools/htslib Additional tools: * perl 5.34.0 +Basic information on how to use this tool: +- executable: htsfile +- help: --help +- version: --version +- description: The htsfile utility attempts to identify what kind of high-throughput sequencing data files the specified files are, and provides minimal viewing capabilities for some kinds of data file. + +Additional information: + +This container includes htslib v1.20 compiled with **libdeflate** for a better cloud performance. + +Full documentation: https://www.htslib.org/doc/samtools.html + ## Example Usage ```bash @@ -22,5 +33,3 @@ ce_tag_padded.sam: SAM version 1.4 sequence text # compresses sample.fastq to sample.fastq.gz in BGZF format (blocked GNU Zip Format) $ bgzip sample.fastq ``` - -Better documentation can be found at [https://www.htslib.org/doc/samtools.html](https://www.htslib.org/doc/samtools.html) diff --git a/samtools/1.20.c/README.md b/samtools/1.20.c/README.md index 9512f1bbe..1317ccb5d 100644 --- a/samtools/1.20.c/README.md +++ b/samtools/1.20.c/README.md @@ -1,14 +1,25 @@ # samtools container -Main tool: +Main tool: [samtools](https://www.htslib.org/) -* [https://www.htslib.org/](https://www.htslib.org/) -* [GitHub](https://github.com/samtools/samtools) +Code repository: https://github.com/samtools/samtools Additional tools: * perl 5.34.0 +Basic information on how to use this tool: +- executable: samtools +- help: --help +- version: --version +- description: Utilities for the Sequence Alignment/Map (SAM) format + +Additional information: + +This container includes samtools v1.20 compiled with **libdeflate** for a better cloud performance. + +Full documentation: https://www.htslib.org/doc/samtools.html + ## Example Usage ```bash @@ -17,4 +28,3 @@ samtools ampliconclip -b bed.file input.bam samtools sort -T /tmp/aln.sorted -o aln.sorted.bam aln.bam ``` -Better documentation can be found at [https://www.htslib.org/doc/samtools.html](https://www.htslib.org/doc/samtools.html) \ No newline at end of file