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Bring mrnaseq instructions up to date (under mrnaseq/) #151

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ctb opened this issue Feb 26, 2015 · 3 comments
Open
8 tasks

Bring mrnaseq instructions up to date (under mrnaseq/) #151

ctb opened this issue Feb 26, 2015 · 3 comments

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@ctb
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ctb commented Feb 26, 2015

  • change from m1.xlarge
  • fix nemo => nema (nematostella)
  • check with @mr-c - is the Debian URL for the adapters stable? (https://sources.debian.net/data/main/t/trimmomatic/0.32+dfsg-2/adapters/TruSeq3-PE.fa)
  • eliminate the use of ${HOME} as on Amazon computers this is too small; OR, mount something there.
  • what does %% do in for loops?
  • remove fastx stuff
  • remove THREADS from filter-abund command as it's not any faster.
  • question @mr-c as to the switch to using multiple directories for the data; this will confuse many people
@mr-c
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mr-c commented Feb 26, 2015

Yes, that URL is stable. I'll file a bug for the adapters to be included in future packages.

%% inside a shell parameter specification causes the trimming from the end of the parameter value of what follows the %%. Just another way to swap out filename extensions; mostly equivalent to your use of basename.

Docs at http://www.gnu.org/software/bash/manual/bash.html#Shell-Parameter-Expansion

I'm very surprised to hear that you think using a subdirectory for each stage of processing will confuse people. I find dozens of files whose names differ by just a few characters in one big directory to be confusing.

@mr-c
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mr-c commented Feb 26, 2015

Trimmomatic bug is filed: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=779296

@ctb
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ctb commented Feb 27, 2015

On Thu, Feb 26, 2015 at 09:54:21AM -0800, Michael R. Crusoe wrote:

I'm very surprised to hear that you think using a subdirectory for each stage of processing will confuse people. I find dozens of files whose names differ by just a few characters in one big directory to be confusing.

Paths/directorys are #1 confusion for people new to the shell, we find.

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