astrobiomike / genelab-utils

GeneLab utils

Some helper programs for NASA GeneLab, such as GL-download-GLDS-data for downloading files from a specific OSD or GLDS ID, and GL-get-workflow for downloading workflows used by GeneLab for processing datasets.

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Conda install

The genelab-utils package should be installed with conda/mamba. If you are not familiar with conda, you can find an introduction here if wanted, and if you are not familiar with mamba, there is a super-short introduction on that same page here if wanted – it's definitely worth using mamba if you use conda at all 👍

conda install -c conda-forge -n base mamba

mamba create -n genelab-utils -c conda-forge -c bioconda -c defaults -c astrobiomike genelab-utils

conda activate genelab-utils

All programs are prefixed with GL- and have a help menu accessible with -h. Version info can be accessed with GL-version.

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Some example pages

• Programmatically downloading GLDS data
  • GL-download-GLDS-data
• Downloading GeneLab workflows
  • GL-get-workflow

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genelab-utils's Issues

GL-validate-raw-data: breaks if "R1" and "R2" are used as part of the sample name

Filenames that use "R1" or "R2" to indicate replicates or other information cause the sample number validation to break.

Given 14 file pairs with "R1" and "R2" present in the file name to designate the replicate number, GL-validate-raw-data returns the following error:

  We expected 14 forward read files, but 16 were found based on currently
  allowed read-pair designations (e.g. these formats: _R1_, _R1., -R1., -R1-,
  .R1., _1.). If it's not clear what the problem is here, share this use-case
  with Mike so we can expand functionality if needed.

GL-gen-file-associations-table needs to reflect latest Metagenomics workflow

Metagenomics workflow as updated to create zip files of the bins and MAGs fasta files for each sample. The associated-file-names.tsv needs to be updated to reflect this change.

ImportError: lxml.html.clean module is now a separate project lxml_html_clean

The above came up when i ran an install on a new system. I don't see a conda version yet, but installing with pip in the environment got around it. pip install lxml_html_clean

Will consider adding that pip install to the conda recipe

GL-est-rRNA-percentages passes incorrect expected_suffix for single-end data

GL-est-rRNA-percentages passes "" as the "expected_suffix" for single-end data, which breaks the snakemake call at line 64 in the Snakefile.

TypeError in file /global/data/temp_scratch/banovak/rRNA-est-percentages-test/current_version/Snakefile, line 64:
can only concatenate str (not "NoneType") to str
  File "/global/data/temp_scratch/banovak/rRNA-est-percentages-test/current_version/Snakefile", line 64, in <module>