organizational page for my various Dockerfiles I use on the desktop and on servers and on work stations
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README.md

README.md

Dockerfiles

(At first I thought the automated build settings at Docker Hub is based on a repo having a single Dockerfile, and so I thought I needed a separate repo for each. But this repo and this one indicate otherwise, and you can see the resulting builds here and here, respectively. Now I sort of wish I didn't remove my recent sub-directory hierarchy. Although if build a bunch together, might sometime encounter Docker Hub's restrictions on how long a build of a repo can be limited to? see here and here for the limits info.)

I want to easily track my Docker efforts, but for now have separate repos for those efforts, and so I made this markdown file to do this.


Dockerfiles for Bioinformatics (Sequence Analysis) Docker images

Dockerfiles for Docker images that make containers (generally linux-based) that aid in performing and documenting replicable (maybe even repeoducible bioinformatics efforts

Associated Docker hub images and github repos

rnaseq_wang:

Complete container for all command line processing as directed in
Using RNA-seq for Analysis of Differential Gene Expression in Fungal Species. Wang C, Schröder MS, Hammel S, Butler G. Methods Mol Biol. 2016;1361:1-40. doi: 10.1007/978-1-4939-3079-1_1. PMID: 26483013

https://hub.docker.com/r/fomightez/rnaseqwang/

https://github.com/fomightez/rnaseq_wang


cufflinks_docker:

Docker container for Cufflinks for Transcriptome assembly and differential expression analysis for RNA-Seq

https://hub.docker.com/r/fomightez/rnaseqcufflinks/

https://github.com/fomightez/cufflinks_docker

bowtie1_docker:

Docker container for Bowtie1 for splicing-unaware aligning of reads and differential expression analysis for RNA-Seq

https://hub.docker.com/r/fomightez/bowtie1/

https://github.com/fomightez/bowtie1_docker



Dockerfiles for Structural Analysis (Structural Bioinformatics) Docker images

Dockerfiles for Docker images that make containers (generally linux-based) that aid in performing analysis of molecular structures

Associated Docker hub images and github repos

CNSsolve1pt21:

Dockerfile to build images that will compile CNSsolve 1.21 (need old version for ultimately working with software at http://aria.pasteur.fr/supplementary-data/x-links)
NOTE: THE FILE cns_solve_1.21_all-mp.tar.gz MUST BE PROVIDED, SEE DOCKEFILE. Besides that, this Dockerfile will handle everything else to result in a freshly compiled version that will run.

https://github.com/fomightez/cnssolve1pt21_docker

XL-MOD:

Dockerfile to build images that will generate a modified CNS 1.21 for running XL-MS Protein assembly (XL-MOD) with a working directory set up as described at http://aria.pasteur.fr/supplementary-data/x-links/readme/view .
NOTE: THE FILE cns_solve_1.21_all-mp.tar.gz MUST BE PROVIDED, SEE DOCKEFILE. Besides that, this Dockerfile will handle everything else to result in modified, freshly compiled CNSsolve 1.21 able to run the scripts for XL-MS Protein assembly (XL-MOD).

https://github.com/fomightez/xlmod_docker



Dockerfiles for Docker images that connect to Mac Desktop

Dockerfiles for Docker images that make containers (generally linux-based) that when run, can display to the screen of a properly set up Mac OSX system.

Associated Docker hub images and github repos

Chromium:

https://hub.docker.com/r/fomightez/chromium/

https://github.com/fomightez/docker-mac-linuxchromium



Dockerfiles for Docker images for other various uses

Dockerfiles for Docker images that make other useful containers.

Associated Docker hub images and github repos

Youtube-DL:

https://hub.docker.com/r/fomightez/youtubedl/

https://github.com/fomightez/youtube-dl_docker