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MontgomeryLab / tinyRNA

tinyRNA provides an all-in-one solution for precision analysis of sRNA-seq data. At the core of tinyRNA is a highly flexible counting utility, tiny-count, that allows for hierarchical assignment of reads to features based on positional information, extent of feature overlap, 5’ nucleotide, length, and strandedness.
GNU General Public License v3.0
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Installation issue fix, lockfile creation script, and tiny-count command line argument updates #226

Closed AlexTate closed 2 years ago

AlexTate commented 2 years ago

Updated the URL in lockfiles for bioconductor-genomeinfodbdata to use the latest build, which fixes an issue in the recipe that prevented tinyRNA installation (many thanks to Tai for tracking this down).

I've also added a script to automate the process of updating the lockfiles per the contents of environment.yml, which will also include updated build numbers for the entire dependency tree. The script can be used to remedy future issues like this. Note that it was NOT used for the lockfile changes included in this PR since the build updates were quite extensive and I have time limitations for testing this week

tiny-count's --features-csv short argument was changed from -c to -f when 3rd party SAM file support was added. This change was made hastily and a bit last minute, and since it was unrelated to the issue I overlooked some necessary updates for the new argument names. The CommandLineTool and Workflow CWL, as well as codebase references, have been updated to reflect this change.

Closes #224

taimontgomery commented 2 years ago

There's a typo in the .lock files (linux line 212, OSX line 190):

https://conda.anaconda.org/bioconda/noarch/bioconductor-genomeinfodbdata-1.2.7-r41hdfd78af_2.tar.bz2#b23c1905f6ee6dddcfa3af515aa4844fs

should be........

https://conda.anaconda.org/bioconda/noarch/bioconductor-genomeinfodbdata-1.2.7-r41hdfd78af_2.tar.bz2#b23c1905f6ee6dddcfa3af515aa4844f

There's an "s" at the end of the md5 that shouldn't be there.

Otherwise, resolves issue-224.