Re: [PATCH 0/4] Add sra-tools.

[ludo@gnu.org (Ludovic Courtès)]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:

> The NCBI project uses a frustrating custom configuration script written
> in Perl, requiring a lot of tweaks to make it work.
>
> More significant changes had to be made to the build of both ncbi-vdb
> and sra-tools, because sra-tools expects the sources and the raw build
> output of ncbi-vdb to lie in some directory.  It would not build against
> an installed version of ncbi-vdb due to missing libraries and missing
> includes.
>
> As both of these projects have been split from the same repository in
> the recent past and are so closely coupled I took the liberty to let
> ncbi-vdb install more headers and more libraries, so that at the time
> sra-tools is built we don't need to rebuild ncbi-vdb just to get at the
> includes and interface libraries.  The phases do not look pretty but
> they are as clean as I could make them.

Sounds reasonable.

> I had to remove libxml2 from the inputs to sra-tools, resulting in a
> failure to build a couple of loader tools.  The reason for this is that
> I encountered linker problems like these:

It looks like an upstream bug?  And why is it being statically-linked
anyway?  It would be nice if they would default to dynamic linking,
which is more efficient in terms of memory use, etc.

> From c80c582724cc515b4baa54623c5c691de01ea2fd Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 14 Apr 2015 14:23:19 +0200
> Subject: [PATCH 1/4] gnu: Add NGS SDK.
>
> * gnu/packages/bioinformatics.scm (ngs-sdk): New variable.

OK!

> +    (synopsis "API for accessing Next Generation Sequencing data")

I would put quotes around “Next Generation”.  :-)

> From f689906b999164282841baafe3ec705a91103ef8 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 14 Apr 2015 14:24:01 +0200
> Subject: [PATCH 2/4] gnu: Add NGS Java bindings.
>
> * gnu/packages/bioinformatics.scm (ngs-java): New variable.

[...]

> +    (synopsis "Java bindings for NGS SDK")
> +    (description
> +     (string-append (package-description ngs-sdk)
> +                    "\n\nThis package contains the Java bindings."))))

‘description’ should be a string literal, otherwise xgettext won’t catch
it, thereby preventing i18n.

What I would do is just keep ‘description’ unchanged, or rewrite it.
Keeping it unchanged is OK here since the synopsis makes it clear that
these are Java bindings.

> From 9e08ad24aa173320c025e6bf2460d95784c74a40 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 14 Apr 2015 14:42:49 +0200
> Subject: [PATCH 3/4] gnu: Add NCBI VDB.
>
> * gnu/packages/bioinformatics.scm (ncbi-vdb): New variable.

OK.

> From 11acd5405931288923e54298ba4d481c2b55211d Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 14 Apr 2015 14:43:32 +0200
> Subject: [PATCH 4/4] gnu: Add sra-tools.
>
> * gnu/packages/bioinformatics.scm (sra-tools): New variable.

OK.

Thanks!

Ludo’.