Re: [PATCH] Add preseq.

2015-07-10 Thread Ricardo Wurmus
Mark H Weaver writes: > No. It's deterministic, and 'modify-phases' is in (guix build utils) so > it can't be changed without triggering a full rebuild. The edits are > done in the order shown, as if it was imperative code. For example: Thank you for confirming the behaviour. >> When I buil

Re: [PATCH] Add preseq.

2015-07-09 Thread Mark H Weaver
Ricardo Wurmus writes: >> ERROR: In procedure mkstemp!: >> ERROR: In procedure mkstemp!: No such file or directory >> builder for `/gnu/store/2ll28ypms57h0k44f4mmclhw9dz3ccvm-preseq-1.0.2.drv' >> failed with exit code 1 >> @ build-failed >> /gnu/store/2ll28ypms57h0k44f4mmclhw9dz3ccvm-preseq-1.0.

Re: [PATCH] Add preseq.

2015-07-09 Thread Ricardo Wurmus
> ERROR: In procedure mkstemp!: > ERROR: In procedure mkstemp!: No such file or directory > builder for `/gnu/store/2ll28ypms57h0k44f4mmclhw9dz3ccvm-preseq-1.0.2.drv' > failed with exit code 1 > @ build-failed /gnu/store/2ll28ypms57h0k44f4mmclhw9dz3ccvm-preseq-1.0.2.drv - > 1 builder for `/gnu/st

Re: [PATCH] Add preseq.

2015-07-08 Thread Mark H Weaver
l...@gnu.org (Ludovic Courtès) writes: > Ricardo Wurmus skribis: > >> From e3bd0a861121c441b44d77d30f2aaddb766b49c2 Mon Sep 17 00:00:00 2001 >> From: Ricardo Wurmus >> Date: Tue, 23 Jun 2015 10:54:00 +0200 >> Subject: [PATCH 2/2] gnu: Add preseq. >> >> * gnu/packages/bioinformatics.scm (preseq):

Re: [PATCH] Add preseq.

2015-07-08 Thread Ludovic Courtès
Ricardo Wurmus skribis: > From b1ba27153faca9bdf46d42046c43f8c60f945368 Mon Sep 17 00:00:00 2001 > From: Ricardo Wurmus > Date: Thu, 2 Jul 2015 15:53:47 +0200 > Subject: [PATCH 1/2] gnu: samtools: Install headers. > > * gnu/packages/bioinformatics.scm (samtools)[arguments]: Add phase > "instal

Re: [PATCH] Add preseq.

2015-07-07 Thread Ricardo Wurmus
>>> Why leave the headers? Isn’t it risky to leave headers that may be >>> different from the Samtools that we’re actually linking against? >> >> The problem is with our Samtools package(s). They don't install >> headers. I'd better update them to install the headers; then I could >> just delete

Re: [PATCH] Add preseq.

2015-07-01 Thread Ludovic Courtès
Ricardo Wurmus skribis: > Ludovic Courtès writes: > >>> + (snippet >>> + ;; Remove bundled samtools. Leave the headers. >>> + '(for-each delete-file >>> + (find-files "preseq-master/samtools" >>> +

Re: [PATCH] Add preseq.

2015-07-01 Thread Ricardo Wurmus
Ludovic Courtès writes: >> + (snippet >> + ;; Remove bundled samtools. Leave the headers. >> + '(for-each delete-file >> + (find-files "preseq-master/samtools" >> + "\\.c$") > > Why leave

Re: [PATCH] Add preseq.

2015-07-01 Thread Ricardo Wurmus
> Attached is a new version that includes support for BAM files, but > without using the bundled version of samtools. Two patches were > necessary that I have submitted upstream. > > I'm still testing this with a user, and I'm waiting for upstream to > comment on the patches, so I'm not in a hurry

Re: [PATCH] Add preseq.

2015-07-01 Thread Ludovic Courtès
Ricardo Wurmus skribis: > From 3ffe6847848f6ba107e0757728f1c6a6e7807d56 Mon Sep 17 00:00:00 2001 > From: Ricardo Wurmus > Date: Tue, 23 Jun 2015 10:54:00 +0200 > Subject: [PATCH] gnu: Add preseq. > > * gnu/packages/bioinformatics.scm (preseq): New variable. [...] > + (snippet > +

Re: [PATCH] Add preseq.

2015-06-25 Thread Ricardo Wurmus
Attached is a new version that includes support for BAM files, but without using the bundled version of samtools. Two patches were necessary that I have submitted upstream. I'm still testing this with a user, and I'm waiting for upstream to comment on the patches, so I'm not in a hurry to push th