Re: Some tasks for people loving Ensembl package
----- Mail original -----
> De: "Andreas Tille" <andreas@an3as.eu>
> À: "Debian Med Project List" <debian-med@lists.debian.org>
> Envoyé: Mercredi 7 Décembre 2011 22:29:37
> Objet: Some tasks for people loving Ensembl package
> [I keep some additional people in Bcc who might not yet subscribed and
> I do not know whether their e-mail address should be exposed to
> spammers]
>
> Hi,
>
> I just commited a very simple typo in an upstream script which should
> be
> reported (otherwise the script might stay broken). Is there any
> volunteer to report this upstream? For the patch either see below[2]
> or
> point upstream to the location in SVN[1].
>
> Further there is another problem which needs clarification from
> upstream.
> The script
>
> ensembl-variation/scripts/import/run.me
>
> is executable and most possibly a shell script but lacking a proper
> shebang line. I admit it is a bit suspicious because it calls to
> programs which most probably do not exist:
>
> 1. bsub (there are some scripts starting with bsub* but not exactly
> this string)
> 2. /usr/local/ensembl/bin/perl --> this should definitely replaced
> by simply calling perl
>
> Is there any volunteer who would take over the job of contacting
> upstream (possibly on behalf of the Debian Med team if this sounds
> more
> convincing) to submit the patch and clarify the issue of the run.me
> script?
I do not have time right now to do so, I am on GMOD Chado stuff which takes quite a lot of time.
However, if no one is volunteer in the meanwhile I will be glad to help (but will be on january)
Olivier
>
> Kind regards
>
> Andreas.
>
>
> [1]
> http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ensembl/ensembl/trunk/debian/patches/fix_usr_bin_env_typo.patch?view=markup
> [2] extract from commit mail:
> ----- Forwarded message from Andreas Tille <tille@alioth.debian.org>
> -----
>
> Date: Wed, 7 Dec 2011 21:06:23 +0000
> From: Andreas Tille <tille@alioth.debian.org>
> To: debian-med-commit@lists.alioth.debian.org
> Subject: r8823 - in trunk/packages/ensembl/ensembl/trunk/debian: .
> patches
>
> Author: tille
> Date: 2011-12-07 21:06:23 +0000 (Wed, 07 Dec 2011)
> New Revision: 8823
>
> ...
> Added:
> trunk/packages/ensembl/ensembl/trunk/debian/patches/fix_usr_bin_env_typo.patch
> ===================================================================
> ---
> trunk/packages/ensembl/ensembl/trunk/debian/patches/fix_usr_bin_env_typo.patch
> (rev 0)
> +++
> trunk/packages/ensembl/ensembl/trunk/debian/patches/fix_usr_bin_env_typo.patch
> 2011-12-07 21:06:23 UTC (rev 8823)
> @@ -0,0 +1,8 @@
> +---
> ensembl-65.orig/ensembl-variation/scripts/misc/generate_reg_file.pl
> ++++ ensembl-65/ensembl-variation/scripts/misc/generate_reg_file.pl
> +@@ -1,4 +1,4 @@
> +-#!/use/bin/env perl
> ++#!/usr/bin/env perl
> +
> + use strict;
> + use warnings;
>
> _______________________________________________
>
> ----- End forwarded message -----
>
> --
> http://fam-tille.de
>
>
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