Re: [PATCH] gnu: Add samtools

2014-12-15 Thread Ludovic Courtès
Ricardo Wurmus skribis: > Can we disable the test suite for certain architectures? Or would they > have to be disabled completely? >>> >>> Since it fails the same way on mips64el, I suggest this instead: >>> >>>#:tests? (string=? (or (%current-system) (%current-target-system)) >>>

Re: [PATCH] gnu: Add samtools

2014-12-15 Thread Ricardo Wurmus
Can we disable the test suite for certain architectures? Or would they have to be disabled completely? >> >> Since it fails the same way on mips64el, I suggest this instead: >> >>#:tests? (string=? (or (%current-system) (%current-target-system)) >> "x86_64-l

Re: [PATCH] gnu: Add samtools

2014-12-13 Thread Mark H Weaver
Mark H Weaver writes: > l...@gnu.org (Ludovic Courtès) writes: > >> Ricardo Wurmus skribis: >> >>> Can we disable the test suite for certain architectures? Or would they >>> have to be disabled completely? >> >> Yes, just pass something like in ‘arguments’: >> >> #:tests? (not (string=? (or (

Re: [PATCH] gnu: Add samtools

2014-12-13 Thread Mark H Weaver
l...@gnu.org (Ludovic Courtès) writes: > Ricardo Wurmus skribis: > >> Can we disable the test suite for certain architectures? Or would they >> have to be disabled completely? > > Yes, just pass something like in ‘arguments’: > > #:tests? (not (string=? (or (%current-system) (%current-target-s

Re: [PATCH] gnu: Add samtools

2014-12-13 Thread Ludovic Courtès
Ricardo Wurmus skribis: > Can we disable the test suite for certain architectures? Or would they > have to be disabled completely? Yes, just pass something like in ‘arguments’: #:tests? (not (string=? (or (%current-system) (%current-target-system)) "i686-linux")) A

Re: [PATCH] gnu: Add samtools

2014-12-13 Thread Ricardo Wurmus
Mark H Weaver writes: > This built successfully on x86_64, but on i686 its test suite shows 87 > failures ("SAM files differ"). See: > > http://hydra.gnu.org/build/173180 > http://hydra.gnu.org/build/173180/log/raw Apparently, these 87 test failures on non-64-bit architectures are upstream pr

Re: [PATCH] gnu: Add samtools

2014-12-12 Thread Mark H Weaver
Ricardo Wurmus writes: > From c4cae6d77e00491cfd78fe03da8ab617bc1732f2 Mon Sep 17 00:00:00 2001 > From: Ricardo Wurmus > Date: Thu, 11 Dec 2014 15:48:22 +0100 > Subject: [PATCH] gnu: Add samtools This built successfully on x86_64, but on i686 its test suite shows 87 failures ("

Re: [PATCH] gnu: Add samtools

2014-12-12 Thread Ludovic Courtès
rer that it’s bioinfo-related? > > I chose to reword it as "Utilities to efficiently manipulate nucleotide > sequence alignments"; is this okay? Sure. > From c4cae6d77e00491cfd78fe03da8ab617bc1732f2 Mon Sep 17 00:00:00 2001 > From: Ricardo Wurmus > Date: Thu, 11

Re: [PATCH] gnu: Add samtools

2014-12-12 Thread Ricardo Wurmus
ling (in >> +conjunction with bcftools), and a simple alignment viewer.") > > Likewise, maybe replace “alignments” with “nucleotide sequence > alignments” or something to that effect? I agree. See attached patch. >From c4cae6d77e00491cfd78fe03da8ab617bc1732f2 Mon Sep 17 0

Re: [PATCH] gnu: Add samtools

2014-12-11 Thread Ludovic Courtès
Ricardo Wurmus skribis: > * gnu/packages/bioinformatics.scm: New file > * gnu-system.am (GNU_SYSTEM_MODULES): Add it Perfect! [...] > +(synopsis "Efficient utilities on manipulating alignments in the SAM > format") What about “Utilities to manipulate nucleotide sequence alignments”, to m

[PATCH] gnu: Add samtools

2014-12-11 Thread Ricardo Wurmus
* gnu/packages/bioinformatics.scm: New file * gnu-system.am (GNU_SYSTEM_MODULES): Add it --- gnu-system.am | 1 + gnu/packages/bioinformatics.scm | 83 + 2 files changed, 84 insertions(+) create mode 100644 gnu/packages/bioinformatics.scm