Subject: Re: [bug#27377] [PATCH] gnu: Add f-seq.

From: Ben Woodcroft <[email-masked]>
Date: Sat, 17 Jun 2017 13:31:55 +1000

Hi Ricardo,

On 16/06/17 01:26, Ricardo Wurmus wrote:
> * gnu/packages/bioinformatics.scm (f-seq): New variable.
> [..]
> +      (synopsis "Feature density estimator for high-throughput sequence tags")
> +      (description
> +       "F-Seq is a software package that generates a continuous tag sequence
> +density estimation allowing identification of biologically meaningful sites
> +whose output can be displayed directly in the UCSC Genome Browser.")
"features" is a little vague for me. How about something like this

"F-Seq is a software package that generates a continuous tag sequence
density estimation allowing identification of biologically meaningful sites such as transcription factor binding sites (ChIP-seq) or regions of open chromatin (DNase-seq). Output can be displayed directly in the UCSC Genome Browser."

I also had some problems running this software in a container:

[env]# fseq
/gnu/store/xjfxqh6rp4y4jwr4smwbvjqnikjbivai-profile/bin/fseq: line 30: 
sed: command not found
/gnu/store/xjfxqh6rp4y4jwr4smwbvjqnikjbivai-profile/bin/fseq: line 32: 
sed: command not found
/gnu/store/xjfxqh6rp4y4jwr4smwbvjqnikjbivai-profile/bin/fseq: line 30: 
sed: command not found
/gnu/store/xjfxqh6rp4y4jwr4smwbvjqnikjbivai-profile/bin/fseq: line 32: 
sed: command not found
/gnu/store/xjfxqh6rp4y4jwr4smwbvjqnikjbivai-profile/bin/fseq: line 62: 
dirname: command not found
Error: Could not find or load main class edu.duke.igsp.gkde.Main

(exitstatus 1)

Given that the exitstatus of the above is non-zero, what about adding a 
cheap and cheerful test phase which simply runs "fseq -h" or similar?

Otherwise LGTM.

ben