Shareef Dabdoub comments

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Shareef Dabdoub

Error during installation: "node.js" on Mac OS with nvm

@iamskok Your PATH setting has 'node' included at the end. Remove that and it should be fine: { "PATH": ":/Users/skok/.nvm/versions/node/v10.9.0/bin" }

Conversion of SAM to BAM using samtools.

Another use for this feature would be to calculate genome coverage with something like [bedtools](https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html).

Ability to add papers by smaller publishers.

Just checking in post-1.0 release. Any updates on the PMC datasource?

Oral Microbiome (eHOMD) kraken-bracken database

Hi Flo, I haven't updated to the latest (10.1) version (should start working on that), but I have a Kraken2+bracken build for v9.15 of eHOMD. Shareef

kmer2read_distr uses omp_get_num_procs() instead of omp_get_num_threads() to check the validity of the -t parameter

Although, after re-compiling with the threads function, it still complains with anything >1, and I have OMP_NUM_THREADS set correctly for building with kraken2, and it works there.

Steps to download all the databases and setup manually in DRAM

Here is the list of databases: - kofam_hmm - kofam_ko_list - uniref - pfam - pfam_hmm - dbcan - dbcan_fam_activities - dbcan_subfam_ec - vogdb - vog_annotations - viral - peptidase...

New release needed

Hi @bgruening Thanks for the notice. I'm working on updating a few things, but I'll try to get a new release out soon. Shareef