From mboxrd@z Thu Jan 1 00:00:00 1970 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) Subject: Re: [PATCH 0/4] Add sra-tools. Date: Fri, 17 Apr 2015 10:16:44 +0200 Message-ID: <87383zdv9v.fsf@gnu.org> References: Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:36148) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Yj1SF-00083N-Gw for guix-devel@gnu.org; Fri, 17 Apr 2015 04:16:52 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Yj1SA-0001X1-Dz for guix-devel@gnu.org; Fri, 17 Apr 2015 04:16:51 -0400 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:40551) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Yj1SA-0001Wv-Ax for guix-devel@gnu.org; Fri, 17 Apr 2015 04:16:46 -0400 In-Reply-To: (Ricardo Wurmus's message of "Tue, 14 Apr 2015 15:00:09 +0200") List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: Ricardo Wurmus Cc: Guix-devel Ricardo Wurmus 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 > 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 =E2=80=9CNext Generation=E2=80=9D. :-) > From f689906b999164282841baafe3ec705a91103ef8 Mon Sep 17 00:00:00 2001 > From: Ricardo Wurmus > 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.")))) =E2=80=98description=E2=80=99 should be a string literal, otherwise xgettex= t won=E2=80=99t catch it, thereby preventing i18n. What I would do is just keep =E2=80=98description=E2=80=99 unchanged, or re= write 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 > 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 > 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=E2=80=99.