This repository contains Dockerfiles I accumulated for different purposes.
Some of the images are bare-bone and should maybe be changed when incorporated into analysis pipelines.
The working directory in these containers is generally /data. This can be used as a bindpoint. Downloaded software is generally kept in /software. Some older containers here may however not follow these rules.
The tags given for each container correspond the the available versions of different programs. The Dockerfiles refer to the latest tags.
Currently available containers:
abyss alitv angsd astral augustus bamutil bbmap beast bedops bedtools bibcure biopython_plus blobtools bmge bonito bowtie2 busco cafe cafe-viz clipkit clustalo colord concoct consent cupp datasets deeploc dentist diamond edta eggnog-mapper emboss ete3 fasta3 fastcodeml fastqc fastuniq ffsend flappie flash fmlrc gatk genome-viz get_organelle gnuplot guidance2 hmmer ima2 imagemagick interproscan-wrapper ipyrad iqtree julia jupyter-lab keras kmergenie macse mafft magic-wormhole mamba maxbin mcl metabat metaxa miniBarcoder mitos mosdepth mrbayes multiqc mummer muscle mutt ncbi-blast ncbi-datasets necat nim nimbio_plus norgal novoplasty oma-standalone ont-fast5-api orthofinder paml pal2nal pandoc pass pear phykit phylobayes phylobayes-mpi phylopy phylo-scripts picard pigz prank purge_haplotigs pyinstaller pyscaf raxml-ng rename rmarkdown repeatmodeler-repeatmasker rphylogenetics samtools scrape_cazy seqtk singularity snakemake spades sra-tools stringtie table2asn tbl2asn tcoffee treeshrink trimal trimmomatic typst ubuntu viralmsa quast quicktree
tags: 2.0rc2, 2.0.7
docker run -v $(pwd):/data reslp/iqtree:2.0.7
tags: 3.2.6
docker run -v $(pwd):/data -it reslp/mrbayes-mpi:3.2.6 /sbin/my_init -- mpirun --allow-run-as-root -np 8 mb /data/alignment.nex
tags: latest
docker run reslp/phylo-scripts:latest
tags: 3.12.0, 3.13.0, 3.15.3
WORKDIR /data
docker pull reslp/spades:3.13.0
tags: 0.38
docker run -t -v $(pwd):/data reslp/trimmomatic:0.38 trimmomatic PE -phred33 -threads 8 /data/pair1.fq.gz /data/pair2.fq.gz /data/trimmed_pair1.fq.gz /data/unpaired_pair1.fq.gz /data/trimmed_pair2.fq.gz /data/unpaired_pair2.fq.gz HEADCROP:20 ILLUMINACLIP:/data/adapters.fa:2:30:10 LEADING:30 TRAILING:30 SLIDINGWINDOW:4:15 MINLEN:80
or
docker run --user $(id -u):$(id -g) --rm -v $(pwd):/data reslp/trimmomatic trimmomatic
Important: The adapter file is not part of the docker image. It needs to passed together with the mounted directory.
tags: 0.11.7
docker run -v $(pwd):/data --rm reslp/fastqc:0.11.7 fastqc /data/illumina_reads_5_R1_trimmed.fq -o /data
docker run --user $(id -u):$(id -g) --rm -v $(pwd):/data reslp/fastqc:0.11.7 fastqc -h
tags: 2.2.6
docker pull reslp/maxbin:2.2.6
docker run --rm reslp/maxbin:2.2.6
tags: 1.1
docker pull reslp/concoct:1.1
docker run --rm reslp/concoct:1.1
A complete example filtering a metagenome. The metagenome.fasta file should be in the current working directory.
docker run -t --user $(id -u):$(id -g) -v $(pwd):/data/ --rm reslp/concoct:1.1 cut_up_fasta.py /data/metagenome.fasta -c 10000 -o 0 --merge_last -b /data/metagenome.fasta_contigs_10K.bed > metagenome.fasta_contigs_10K.fa
docker run -t --user $(id -u):$(id -g) -v $(pwd):/data/ --rm reslp/concoct:1.1 concoct_coverage_table.py /data/metagenome.fasta_contigs_10K.bed /data/metagenome.fasta.bam > concoct_coverage_table.tsv
docker run -t --user $(id -u):$(id -g) -v $(pwd):/data/ --rm reslp/concoct:1.1 concoct --composition_file /data/metagenome.fasta_contigs_10K.fa --coverage_file /data/concoct_coverage_table.tsv -b /data/concoct/metagenome.fasta_concoct --threads 24
docker run --user $(id -u):$(id -g) -v $(pwd):/data/ --rm reslp/concoct:1.1 merge_cutup_clustering.py /data/concoct/metagenome.fasta_concoct_clustering_gt1000.csv > concoct/metagenome.fasta_concoct_clustering_merged.csv
docker run -t --user $(id -u):$(id -g) -v $(pwd):/data/ --rm reslp/concoct:1.1 extract_fasta_bins.py /data/metagenome.fasta /data/concoct/metagenome.fasta_concoct_clustering_merged.csv --output_path /data/concoct/bins
tags: 2.13
docker run --rm reslp/metabat:2.13
tags: 3.0.2, 4.1.4, 5.2.1
The command for busco >4 is busco instead of run_busco on busco <4.
docker run --rm reslp/busco:3.0.2
docker run --rm reslp/busco:4.1.4
tags: 1.1.1
These commands expect that blast results are alread present:
docker run -t --user $(id -u):$(id -g) -v $(pwd):/data/ --rm reslp/blobtools:1.1.1 create -i /data/metagenome.fasta -b /data/metagenome.fasta.bam -t /data/blobtools/metagenome.fasta_diamond_matches_formatted -o /data/blobtools/metagenome.fasta_blobtools
docker run -t --user $(id -u):$(id -g) -v $(pwd):/data/ --rm reslp/blobtools:1.1.1 view -i /data/blobtools/metagenome.fasta_blobtools.blobDB.json -o /data/blobtools/
docker run -t --user $(id -u):$(id -g) -v $(pwd):/data/ --rm reslp/blobtools:1.1.1 plot -i /data/blobtools/metagenome.fasta_blobtools.blobDB.json -o /data/blobtools/
tags: 5.0.2
Run QUAST on all fasta files in current directory:
docker run --rm -t -v $(pwd):/data/ reslp/quast:5.0.2 quast.py $(ls -d -1 "*.fasta" | sed 's/^/\/data\//') -o /data/quast --silent
tags: 2.9.0, 2.15.0
To create a blast database and run a blastp search:
my_sequences.fastaand sequences_to_search.faneed to be in the current working directory. The blastdb will also be created there.
docker run --rm -v $(pwd):/files/ reslp/ncbi-blast:2.9.0 makeblastdb -in /files/my_sequences.fasta -dbtype 'prot' -hash_index -out /files/my_blastdb
docker run --rm -v $(pwd):/files/ reslp/ncbi-blast:2.9.0 blastp -db /files/my_blastdb -query /files/sequences_to_search.fa -outfmt 6 > blast_results.txt
tags: 3.4.1, 3.6.3
To run the conatiner and to be able to run singularity containers inside it docker needs to be run with privileged mode:
docker run --privileged -it --rm -v $(pwd):/data --entrypoint /bin/bash reslp/singularity:3.4.1
Inside the container it is now possible to run singularity images. For example the singularity image for funannotate (which was downloaded and converted to .sif from Docker Hub).
singularity run funannotate.sif mask -i Trapelia_coarctata_sorted.fas -o Trapelia_coarctata_mask.fas -m repeatmasker
tags: 1.0.3, 2.0.1
docker pull reslp/eggnog-mapper:2.0.1
docker run reslp/eggnog-mapper:2.0.1
tags: 5.7.1
docker pull reslp/astral:5.7.1
docker run -it --rm reslp/astral:5.7.1 java -jar /ASTRAL-5.7.1/Astral/astral.5.7.1.jar
tags: 14
docker pull reslp/pal2nal:14
docker run -it reslp/pal2nal:14
tags: 7.464
docker run -it --rm -v $(pwd):/data reslp/mafft:7.464 mafft --auto --quiet /data/OG0000331.fa > OG0000331_aligned.fa
tags: 1
Containerized version of a python script to download information from CAZY.org:
docker run -it --rm reslp/scrape_cazy:1
docker run --rm -it -v $(pwd):/data reslp/scrape_cazy:1 scrape_cazy.py -f GH3
tags: 1.0
This container needs some things set up properly to work:
- Download DeepLoc: https://services.healthtech.dtu.dk/software.php
- Change the first line in
bin/deeplocto#!/usr/bin/env python - Mind that you correctly use the bindpoints of the container on execution:
docker run --rm -it -v $(pwd)/deeploc-1.0/bin:/external -v $(pwd)/deeploc-1.0/DeepLoc:/usr/lib/python3/dist-packages/DeepLoc -v $(pwd):/data reslp/deeploc:1.0 deeploc -f /data/deeploc-1.0/test.fasta
Correct long reads: https://github.com/morispi/CONSENT
tags: v2.1
docker run --rm -v $(pwd):/corrected reslp/consent:v2.1 CONSENT-correct --in /corrected/Lmin_combined.fasta --out /corrected/Lmin_combined_corrected.fasta --type ONT
Correct long reads: https://github.com/holtjma/fmlrc
tags: v1.0.0
docker run reslp/fmlrc:v1.0.0
This image should serve as a base environment to execute python scripts which use biopython and scipy. Tag version corresponds to biopython.
tags: 1.77
docker run reslp:biopython_plus:1.77
This is a dockerfile for: https://github.com/asrivathsan/miniBarcoder
tags: 5e1dc3b
docker run --rm -it --entrypoint /bin/bash reslp/minibarcoder:5e1dc3b
tags: 2.2
WORKDIR is /data
docker run --rm -it -v $(pwd):/data reslp/metaxa:2.2
tags: 4.1c
WORDIR is /data
docker run --rm -it -v $(pwd):/data reslp/phylobayes:4.1c
tags: 1.8b, git_dca7bdf, c12c4d7, 3c77656 (commit from Feb 2023)
WORDIR is /data
docker run --rm -it -v $(pwd):/data reslp/phylobayes-mpi:c12c4d7
tags: 2.02
WORDIR is /data
docker run --rm -it -v $(pwd):/data reslp/guidance2:2.02
tags: 1.0.0, 1.1.0
WORKDIR is /data
docker run --rm -it -v $(pwd):/data reslp/raxml-ng:1.1.0
The tags versions correspond to the R version.
tags: 3.6.3, 4.0.3
docker run --rm -it -v $(pwd):/data reslp/rmarkdown:3.6.3 Rscript -e "rmarkdown::render('./report.rmd')"
The Fast Cross-Platform Package Manager (https://github.com/mamba-org/mamba)
This can serve as a base image for things installed using conda and mamba.
tags: 0.5.3, 0.6.0, 0.7.0, 0.15.3, 0.21.1, 0.23.1, 0.25.0, 1.4.1, 1.5.2(broken!)
docker run --rm -it reslp/mamba:1.4.1
tags: 2.2.5
WORKDIR is /data
docker run --rm -it reslp/abyss:2.2.5
tags: 1.7051
docker run --rm -it reslp/kmergenie:1.7051
This is based on the official ubuntu image and containes build-essential, vim and wget and gdb.
tags: 20.04
docker run --rm -it reslp/ubuntu:20.04
Software for Computational Analysis of gene Family Evolution
tags: 4.2.1, 5.0.0b2, 5.1.0
WORKDIR /data (5.0.0b2, 5.1.0)
docker run --rm -it reslp/cafe:4.2.1
docker run --rm -it -v $(pwd):/data reslp/cafe:5.0.0b2 cafe
tags: 3.1b2
docker run --rm -it -v $(pwd):/data reslp/hmmer:3.1b2 /bin/bash
tags: 6.6.0
docker run --rm -it -v $(pwd):/data reslp/emboss:6.6.0 /bin/bash
tags: 3.3.3
docker run --rm -it $(pwd):/data reslp/augustus:3.3.3
tags: 1.2.4
docker run --rm -it reslp/clustalo:1.2.4
tags: 2.29.2
docker run --rm -it reslp/bedtools:2.29.2
tags: 1.7.1
docker run --rm -it reslp/getorganelle:1.7.1 get_organelle_from_reads.py
tags: 1.9, 1.11
docker run --rm -it reslp/samtools:1.11
tags: 1.4.1
docker run --rm -it -v $(pwd):/data reslp/trimal:1.4.1 trimal -in /data/aligned_all_PF00083.fas -out /data/trimmed_all_PF00083.fas -gappyout
tags: 20201119, 1.26.678
Program had no good versioning while in beta, till it was released tags are build dates.
docker run --rm -it -v $(pwd):/data reslp/table2asn:1.26.678 table2asn -h
tags: 25.8
This is the legacy version of the NCBI tool.
docker run --rm -it -v $(pwd):/data reslp/tbl2asn:25.8
tags: 4de542f
WORKDIR /data
For convenience the flappy container now also includes ont-fast5-api v. 3.1.6.
## see also ont-fast5-api container on how to convert multi-read fast5 (which is the current read type) to single-read fast5.
docker run --rm -it -v $(pwd):/data reslp/flappie:4de542f flappie --help
docker run --rm -it -v $(pwd):/data reslp/flappie:4de542f flappie /data/fast5_single/0/ > 0.fastq
## using ont-fast5-api:
docker run --rm -it -v $(pwd):/data reslp/flappie:4de542f multi_to_single_fast5 -i /data/fast5_pass -s /data/fast5_single -t 4
tags: 3.1.6
## this will convert multi-read fast5 (newer Minion read type) to single-read fast5. See here: https://github.com/nanoporetech/flappie/issues/32
docker run --rm -it -v $(pwd):/data reslp/ont-fast5-api:3.1.6 multi_to_single_fast5 -i /data/fast5_pass -s /data/fast5_single -t 4
tags: 4.0.0beta2
WORKDIR /data
docker run --rm -it -v $(pwd):/data reslp/mummer:4.0.0beta2
tags: 0.3.2
WORKDIR /data
This container works only with CPUs not GPUs. To basecall Minion reads run this:
docker run --rm -i -v $(pwd):/data reslp/bonito:0.3.2 bonito basecaller dna_r9.4.1@v2 --use_openvino --device=cpu /data/fast5_pass 1> basecalls.fasta
docker run --rm -i -v $(pwd):/data reslp/bonito:0.3.2 bonito basecaller dna_r9.4.1@v3 --use_openvino --device=cpu /data/fast5_pass 1> basecalls.fasta
docker run --rm -i -v $(pwd):/data reslp/bonito:0.3.2 bonito basecaller dna_r9.4.1@v2 --use_openvino --device=cpu /data/fast5_pass --fastq 1> basecalls.fastq
tags: 5.39-77.0, 5.48-83.0
This is a wrapper container for use with interproscan. Interproscan is huge so it can't be properly packed into a container. The tags refer to the tested versions of interproscan which work with this container. The dockerfile provided may not be the same for different tags. For older versions, Ubuntu 18.04 is used as base due to MobiDBs incompatibility with python >3.8.2 (see here: ebi-pf-team/interproscan#147). Newer versions of the container are based on Ubuntu 20.04 which has python 3.8.5. Older versions of interproscan (before 5.39-77.0) may not be compatible because they may have again different requirements.
docker pull reslp/interproscan-wrapper:5.39-77.0
https://github.com/lpryszcz/pyScaf
tags: 0.12a4
WORKDIR /data
docker run -v $(pwd):/data -it --rm reslp/pyscaf:0.12a
Extensive de-novo TE annotator - https://github.com/oushujun/EDTA
tags: 1.9.6, 1.9.9, 2.0.1
WORKDIR /data
This container uses rmblast 2.9.0 to make the conda installed repeatmasker work, version 2.10.0 won't work. Also, for edta to work in singularity, the configure perl script of RepeatMasker needs to be executed again.
docker run --rm -it reslp/edta:1.9.6
high performance genomic feature operations - https://github.com/bedops/bedops
tags: 2.4.39
WORKDIR /data
docker run -v $(pwd):/data --rm -it reslp/bedops:2.4.39
Mitochondrial genome assembler - https://bitbucket.org/kosaidtu/norgal/src/master/
tags: 1.0
WORDIR /data
docker run -v $(pwd):/data --rm -it reslp/norgal:1.0 norgal
docker run -v $(pwd):/data --rm -it reslp/norgal:1.0 norgal.py
FASTA and FASTQ processing tool - https://github.com/lh3/seqtk
tags: 1.3
WORKDIR /data
docker run -v $(pwd):/data --rm -it reslp/seqtk:1.3 seqtk
The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. - https://github.com/ncbi/sra-tools
tags: 2.20.1, 2.10.9
WORKDIR /data
docker run --rm -it reslp/sra-tools:2.10.9 fastq-dump
Fast implementation of the neighbour-joining phylogenetic inference method - https://github.com/khowe/quicktree
tags: 2.5
WORKDIR /data
docker run --rm -it reslp/quicktree:2.5
Splice-aware global aligner for DNA and RNA sequencing reads - https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbmap-guide/
tags: 38.90
WORKDIR /data
docker run --rm -it -v $(pwd):/data reslp/bbmap:38.90 bbmap.sh
The organelle assembler and heteroplasmy caller - https://github.com/ndierckx/NOVOPlasty
tags: 4.2
WORKDIR /data
docker run --rm -it -v $(pwd):/data reslp/novoplasty:4.2
docker run --rm -it -v $(pwd):/data reslp/novoplasty:4.2 NOVOPlasty.pl
MITOS is a tool for the annotation of metazoan mitochondrial genomes. - https://gitlab.com/Bernt/MITOS
tags: 2.0.8, 1.0.5
WORKDIR /data
docker run --rm -it -v $(pwd):/data reslp/mitos:2.0.8 runmitos.py
docker run --rm -it -v $(pwd):/data reslp/mitos:2.0.8
This is an R container with some phylogenetic packages preinstalled. It is based on my rmarkdown container. Packages: ape, phytools, wesanderson, RColorBrewer
tags: 4.0.3 (refers to used R version), 4.0.3-strict-versions (with more strict versioning of R packages)
WORKDIR /data
docker run --rm -it -v $(pwd):/data reslp/rphylogenetics:4.0.3
OrthoFinder: phylogenetic orthology inference for comparative genomics
tags: 2.3.3, 2.5.2, 2.5.4, 2.5.5
Note: The version 2.5.4 of orthofinder seems to have a problem with formatting trees. This seems to be related to this. Although in my container the python version is 3.9. Up to stride orthofinder seems to run correctly.
WORKDIR /data
docker run --rm -it -v $(pwd):/data reslp/orthofinder:2.5.5
This Jupyter Lab Notebook also has Tensorflow, Scikitlearn, pandas and numpy installed. The tags refer to the tensorflow version.
tags: 2.4.1
To start a server (either jupyter lab or jupyter notebook):
docker run -d --rm -p 8888:8888 reslp/jupyter-tf:2.4.1 jupyter-lab
docker run -d --rm -p 8888:8888 reslp/jupyter-tf:2.4.1
This will return a hash. Run docker logs on that hash to see the access token. eg:
docker logs 406f5662e0a0fb544ed80d95054642e55439f6eb18fcae30487c8488159e36e4
CUPP is a new approach for sequence analysis based on the hypothesis that conserved peptide patterns can be used to identify similarities between proteins. - https://www.bioengineering.dtu.dk/english/ResearchNy/Research-Sections/Section-for-Protein-Chemistry-and-Enzyme-Technology/Enzyme-Technology/CUPP
tags: 1.0.14
docker run --rm -it reslp/cupp:1.0.14 python /software/CUPP_v1.0.14/CUPPprediction.py --help
IM is a program, written with Rasmus Nielsen, for the fitting of an isolation model with migration to haplotype data drawn from two closely related species or populations. - https://bio.cst.temple.edu/~tuf29449/software
tags: 8.27.12
WORKDIR /data
docker run --rm -it reslp/ima2:8.27.12
AliTV is a program to visualize whole genome alignments: https://alitv.readthedocs.io/en/latest/manual.html
tags: d06bd45
WORKDIR /data
docker run --rm -it -v $(pwd):/data reslp/alitv:d06bd45
This a command line program which performs network speedtests: https://www.speedtest.net/de/apps/cli
tags: 2.1.2, 2.1.3
docker run --rm reslp/speedtest-cli:2.1.3 speedtest-cli --csv >> /home/pi/speedtest/speedtest_data.txt
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. - https://github.com/BenLangmead/bowtie2
tags: 2.3.5
WORKDIR /data
docker run reslp/bowtie2:2.3.5 bowtie2
an ultrafast de novo duplicates removal tool for paired short DNA sequences - https://sourceforge.net/projects/fastuniq/
tags: 1.1
WORKDIR /data
docker run --rm -it reslp/fastuniq:1.1 fastuniq
Fast Length Adjustment of SHort reads - https://ccb.jhu.edu/software/FLASH/
tags: 1.2.11
WORKDIR /data
docker run --rm -it reslp/flash:1.2.11 flash
Programs that perform operations on SAM/BAM files, all built into a single executable, bam. - https://genome.sph.umich.edu/wiki/BamUtil
tags: 1.0.15
WORKDIR /data
docker run --rm -it reslp/bamutil:1.0.15 bam
Java tools for working with NGS data in the BAM format - http://broadinstitute.github.io/picard/
tags: 2.18.7
WORKDIR /data
docker run --rm -it reslp/picard:2.18.7 picard
Genome analysis toolkit - https://gatk.broadinstitute.org/hc/en-us
tags: 3.8
WORKDIR /data
Hint: Executable name is gatk3 NOT gatk!
docker run --rm -it reslp/gatk:3.8 gatk3
ANGSD is a software for analyzing next generation sequencing data - http://www.popgen.dk/angsd/index.php/ANGSD
tags: 0.935
docker run --rm -it reslp/angsd:0.935 angsd
Pipeline to help with curating heterozygous diploid genome assemblies - https://bitbucket.org/mroachawri/purge_haplotigs/src/master/
tags: 1.1.1
WORKDIR /data
docker run --rm -it $(pwd):/data reslp/purge_haplotigs:1.1.1
The FASTA package - protein and DNA sequence similarity searching and alignment programs
tags: 36.3.8
WORKDIR /data
Hint: All the programs of the FASTA3 package have 36 appended to the end of their name. So eg. glsearch is glsearch36 in this container.
docker run --rm -it -v $(pwd):/data reslp/fasta3:36.3.8 glsearch36 /data/query.fas /data/subset.fasta
MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons.
WORKDIR /data
tags: 1.2, 2.05
docker run --rm -it reslp/macse:1.2 macse
docker run --rm -it reslp/macse:2.05 macse -h
julia - The Julia Programming Language
This container includes julia and a number of packages from BioJulia and packages for data handling, plotting and report generation.
tags: 1.6.3
WORDKIR /data
docker run --rm -it reslp/julia:1.6.3 julia
Nim programming lanuage
tags: 1.4.8, 1.6.6, 1.6.12
docker run --rm -it reslp/nim:1.6.6
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing (https://github.com/brentp/mosdepth)
tags: 0.3.3
docker run --rm -it reslp/mosdepth:0.3.3
Reference-guided multiple sequence alignment of viral genomes (https://github.com/niemasd/ViralMSA)
Note: There is an offical container, but it lacks several dependencies and does not work (tested March 21, 2022) hence the container here which largely builds on the official version.
tags: 1.1.20
WORKDUT /data
docker run --rm -it reslp/viralmsa:1.1.20 ViralMSA.py -h
Close assembly gaps using long-reads at high accuracy. (https://github.com/a-ludi/dentist)
Note: This container also includes snakemake 6.0.2 so it is possible to run the whole dentist pipeline within the container.
tags: 3.0.0
docker run --rm -it reslp/dentist:3.0.0 dentist
Multiple sequence alignment with top benchmark scores scalable to thousands of sequences. (https://github.com/rcedgar/muscle)
tags: 5.1
WORKDIR /data
docker run --rm -it reslp/muscle:5.1 muscle
NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. (https://github.com/xiaochuanle/NECAT)
tags: 0.0.1_update20200803
WORKDIR /data
The script in the container is called necat not necat.pl.
docker run --rm -it reslp/necat:0.0.1_update20200803 necat
A versatile compressor of third generation sequencing reads. (https://github.com/refresh-bio/colord)
tags: 1.1.0
WORKDIR /data
docker run --rm -it reslp/colord:1.1.0 colord
BMGE (Block Mapping and Gathering with Entropy) is a program that selects regions in a multiple sequence alignment that are suited for phylogenetic inference. (https://bioweb.pasteur.fr/packages/pack@BMGE@1.12/)
tags: 1.12
WORKDIR /data
docker run --rm -it reslp/bmge:1.12 bmge
A Python framework for the analysis and visualization of trees. - http://etetoolkit.org/
tags: 3.1.2
Hint: External programs don't work due to the omnipresent bug in ete3: etetoolkit/ete#444
WORKDIR /data
docker run --rm -it reslp/ete3:3.1.2
DendroPy Phylogenetic Computing Library - https://dendropy.org/
tags: 4.5.2
WORKDIR /data
docker run --rm -it reslp/dendropy:4.5.2
A container with dendropy, ete3 and pandas based on python 3.7.
tags: 1
WORKDIR /data
docker run --rm -it reslp/phylopy:1
Easily and securely share files from the command line. A fully featured Firefox Send client. https://github.com/timvisee/ffsend
tags: 0.2.76
WORKDIR /data
docker run --rm -it -v $(pwd):/data reslp/ffsend:0.2.76 ffsend upload myfile.txt
Get things from one computer to another, safely. https://github.com/magic-wormhole/magic-wormhole
tags: 0.12.0
WORKDIR /data
docker run --rm -it reslp/magic-wormhole:0.12.0
A universal document converter. https://pandoc.org/
tags: 2.18, 3.1.3
WORKDIR /data
docker run --rm -it -v $(pwd):/data reslp/pandoc:2.18 pandoc test.md -o test.pdf
Bayesian Evolutionary Analysis by Sampling Trees - https://github.com/CompEvol/beast2
tags: 2.6.7
WORKDIR /data
docker run --rm -it -v $(pwd):/data reslp/beast:2.6.7
Parallel implementation of gzip
tags: 2.6
WORKDIR /data
docker run --rm -it -v $(pwd):/data reslp/pigz:2.6
Rename files
tags: 1.10-1
WORKDIR /data
docker run --rm -it -v $(pwd):/data reslp/rename:1.10-1
PyInstaller bundles a Python application and all its dependencies into a single package.
tags: 5.1, 6.1
WORKDIR /data
docker run --rm -it -v $(pwd):/data reslp/pyinstaller:5.1
PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger
tags: 0.9.6
WORKDIR /data
docker run --rm -it reslp/pear:0.9.6
A Practical and Efficient NCBI Taxonomy Toolkit - https://github.com/shenwei356/taxonkit
tags: 0.12.0
WORKDIR /data
docker run --rm -it reslp/taxonkit:0.12.0
Exonerate - A generic tool for pairwise sequence comparison / alignment
tags: 2.4.0
docker run --rm -it reslp/exonerate:2.4.0
Standalone version of the OMA Orthology Matrix - https://omabrowser.org/oma/home/
tags: 2.5.0
WORKDIR /data
docker run --rm -it reslp/oma-standalone:2.5.0 OMA
This container contains RepeatModeler and Repeatmasker including all dependencies (hopefully).
The tag consists of the repeatmodeler version and the repeatmasker version:
tags: 2.0.3-4.1.3
WORKDIR /data
docker run --rm -it reslp/repeatmodeler-repeatmasker:2.0.3-4.1.3
Open source CLI email client
tags: 3.2.6
docker run --rm -it --user $(id -u):$(id -g) -v /etc/passwd:/etc/passwd:ro -v /etc/group:/etc/group:ro -v $HOME/:/home/$USER/ -e HOME=/home/$USER reslp/mutt:3.2.6 mutt
Phylogenetic Analysis by Maximum Likelihood - https://github.com/abacus-gene/paml
tags: 4.9 (conda version, comes with biopython1.81 scipy), 4.10.6
WORKDIR /data
docker run --rm -it reslp/paml:4.10.6
the standard unix password manager - https://www.passwordstore.org/
HOME /data
GnuPG and pass needs to be configured correctly for this to work.
## linux
docker run --rm -it -v $HOME:/data --user $(id -u):$(id -g) reslp/pass:1.7.4
## mac
docker run --rm -it -v $HOME:/data reslp/pass:1.7.4
The Snakemake workflow management system - https://snakemake.readthedocs.io/en/stable/
tags: 6.0.2
docker run --rm -it reslp/snakemake:6.0.2
My own nimbio library together with nim, glob, ggplotnim, clapfn, nimx
tags: 0.0.1, 0.0.2, 0.0.3
docker run --rm -it reslp/nimbio_plus:0.0.2
FastCodeML is a software to infer positive selection along positions of a protein coding gene using the Branch-Site model of evolution - https://bioweb.pasteur.fr/packages/pack@FastCodeML@1.1.0
tags: 1.1.0
docker run --rm -it reslp/fastcodeml:1.1.0 fast
Accelerated BLAST compatible local sequence aligner. - https://github.com/bbuchfink/diamond
tags: 0.9.22, 2.0.7, 2.1.7
WORKDIR /data
docker run --rm -it reslp/diamond:2.0.7
MCL - a cluster algorithm for graphs - https://github.com/micans/mcl
tags: 14.137, 22.282
WORKDIR /data
docker run --rm -it reslp/mcl:14.137
Tools for visualizing cafe output. Currently includes:
cafeplotter and CAFE_Fig
https://github.com/moshi4/CafePlotter
https://github.com/LKremer/CAFE_fig
tags: 1.0
WORKDIR /data
docker run --rm -it reslp/cafe-viz:1.0 cafeplotter
docker run --rm -it reslp/cafe-viz:1.0 python3 /usr/bin/CAFE_fig.py
a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies - https://github.com/jlsteenwyk/phykit
tags: 1.11.15
WORKDIR /data
docker run --rm -it reslp/phykit:1.11.15 phykit -h
a python script to visualize genome assemblies - https://github.com/reslp/genomics
tags: 1.0
docker run --rm -it reslp/genome-viz:1.0 genome_viz.py
Bibcure helps in boring tasks by keeping your bibfile up to date and normalized...also allows you to easily download all papers inside your bibtex. - https://github.com/bibcure/bibcure
tags: 0.3.0
WORKDIR /data
docker run --rm -it -v $(pwd):/data reslp/bibcure:0.3.0 doi2bib -i literature_only_dois.txt -o bib.txt
Sorts amplicons from Nanopore sequencing data based on similarity - https://github.com/avierstr/amplicon_sorter
Tags are based on git commits, since there is no versioning. tags: 33f0d38, c811f09
INFO: The c811f09 is based on my own fork of amplicion_sorter. I added a feature there to change the limit of reads used to create and save the consensus alignment through the -rc flag. This flag does not exist in the official amplicon_sorter.
docker run --rm -it -v $(pwd):/data reslp/amplicon_sorter:33f0d38 amplicon_sorter.py
A new markup-based typesetting system that is powerful and easy to learn. - https://github.com/typst/typst
tags: 0.7.0, 0.9.0, 8c813cb (post line numbers!)
WORKDIR /data
docker run --rm -it -v $(pwd):/data reslp/typst:0.9.0 typst watch /data/document.typ
Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms. - http://www.gnuplot.info/
tags: 5.4.9
docker run --rm -it reslp/gnuplot:5.4.9
Download files from NCBI Entrez by accession - https://github.com/kblin/ncbi-acc-download/
tags: 0.2.8
WORKDIR /data
docker run --rm -it -v $(pwd):/data reslp/ncbi-acc-download:0.2.8 ncbi-acc-download
Transcript assembly and quantification for RNA-Seq - https://github.com/gpertea/stringtie
tags: 2.2.1
WORKDIR /data
docker run --rm -it -v $(pwd):/data reslp/stringtie:2.2.1 stringtie
ImageMagick is a free, open-source software suite, used for editing and manipulating digital images. - https://imagemagick.org/index.php
tags: 7.1.0_46
WORKDIR /data
docker run --rm -it -v $(pwd):/data reslp/imagemagick:7.1.0_46 convert
Tectonic is a modernized, complete, self-contained TeX/LaTeX engine, powered by XeTeX and TeXLive. - https://tectonic-typesetting.github.io/en-US/
tags: 0.14.1
WORKDIR /data
docker run --rm -it -v $(pwd):/data reslp/tectonic:0.14.1 tectonic
Aggregate results from bioinformatics analyses across many samples into a single report - https://multiqc.info/
tags: 1.6, 1.17 (broken), 1.25.1
WORKDIR /data
docker run --rm -it reslp/multiqc:1.25.1 multiqc
These containers come with the deep-learing library KERAS together with several additional libraries such as pandas, numpy, sci-kit and scikit-learn, matplotlib etc.
tags: 3.0.0-torch, 3.0.0-tf
docker run --rm -it reslp/keras:3.0.0-tf
TreeShrink is an algorithm for detecting abnormally long branches in one or more phylogenetic trees. - https://github.com/uym2/TreeShrink
tags: 1.3.9
WORKDIR /data
docker run --rm -it reslp/treeshrink:1.3.9 run_treeshrink -h
Interactive assembly and analysis of RAD-seq data sets - https://github.com/dereneaton/ipyrad
tags: 0.9.93
WORKDIR /data
docker run --rm -it reslp/ipyrad:0.9.93 ipyrad
NCBI Datasets command-line clients - https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install/
tags: 16.25.0
docker run --rm -it reslp/ncbi-datasets:16.25.0 datasets
A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures. - https://github.com/cbcrg/tcoffee
tags: 11.0.8, v.13.46.0.919e8c6b
docker run --rm -it reslp/tcoffee:13.46.0.919e8c6b t_coffee
Alignment trimming software for phylogenetics. - https://github.com/jlsteenwyk/clipkit
tags: 2.3.0
docker run --rm -it reslp/clipkit:2.3.0 clipkit
PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. - https://ariloytynoja.github.io/prank-msa/
tags: v150803
docker run --rm -it reslp/prank:v150803 prank
The NCBI Datasets command-line tools (CLI) - https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install/
tags: 2
docker run --rm -it reslp/datasets:2 datasets