DEVLOG.txt

[2017.04.03] {Testing bioinformatics softwares}
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Some candidates:

 * raxml  - takes alignments
     - worked fine from the first

 * BWA - align fastq reads to (in our sample run) wMel
     - Internal paralellism, problems.
     - /dev/shm/bwactl problems
     - fixed by older minor release.

 * mothur -
    - Internal paralellism, but seems to support sequnetial semantics
    - log file races, don't run twice from the same dir.

 * hmmer - hmm build builds an hmm from an aligned file
           (machine learning), second phase is a searching one and
           requires a larger database
    - Internal paralellism, problems.  Started an hmmer_hacks repo to
      excise the internal parallelism.

 * clustal - can use the alignments, same as raxml
    - works fine on first try

 * bowtie - alignment and other things.  python scripts around C++
          executables.
    - 
 
 * breseq - SNP analysis