Ricardo Wurmus <[email protected]> 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 <[email protected]> > 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 <[email protected]> > 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 <[email protected]> > 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 <[email protected]> > 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’.
