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This queue is for tickets about the Bio-SamTools CPAN distribution.

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Id: 87175
Status: new
Priority: 0/
Queue: Bio-SamTools

Owner: Nobody in particular
Requestors: bayerlein [...]

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Severity: (no value)
Broken in: (no value)
Fixed in: (no value)

Subject: Bio::DB::Sam problems
Date: Tue, 23 Jul 2013 12:22:48 +0200
To: bug-Bio-SamTools [...]
From: Markus Bayerlein <bayerlein [...]>
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Hello. I am using your nice Bio::DB::Sam Perl module to access BAM files to view the data in our Genome Browser. Up to now, the BAM files were uploaded and stored locally on our harddisk. But now I would like to access BAM files remotely via HTTP. I should mention that I do not have the latest version of Bio::DB::Sam installed, but version 1.33 Unfortunately I encounter two problems: 1. When my script is run in taint-mode, it crashes with the error: [SIGDIE] Insecure dependency in chdir while running with -T switch at /usr/lib/perl5/Bio/DB/ line 2233. It seems that the return value of the 'getcwd' function you are calling in line 2229 (in sub index_open_in_safewd) is tainted. This is not a critical issue, as I could run the script without the -T switch. 2. The second problem arises from the usage of the File::Spec->tmpdir method. This method returns the same value for each call from within the same program, i.e. it caches the first value it returns, and keeps this value for every other call. This means that changing the temporary directory (by setting $ENV{TMPDIR}) is possible only once in a program. (Even if $ENV{TMPDIR} was not modified, the return value of File::Spec->tmpdir is sticky after the first call to it, meaning that the method will always return '/tmp'.) However, setting $ENVP{TMPDIR} should be possible once per script. But if Bio::DB::Sam is involved, this seems no longer to be true. I tested this with the following Perl code: - use strict; use File::Spec; BEGIN { $ENV{TMPDIR} = '/home/bayerlein'; } use Bio::DB::Sam; print "tmpdir: ", File::Spec->tmpdir, "\n"; -> prints: tmpdir: /home/bayerlein - while this code: - use strict; use File::Spec; use Bio::DB::Sam; $ENV{TMPDIR} = '/home/bayerlein'; print "tmpdir: ", File::Spec->tmpdir, "\n"; -> prints: tmpdir: /tmp - So the modification of $ENV{TMPDIR} is only effective if it is ensured to take place BEFORE Bio::DB::Sam is loaded. Unfortunately, I cannot ensure this in my application. This means that I cannot change the directory where the BAM index file is saved (by 'index_open_in_safewd'). But in my application it is important to decide where to save the index file (to avoid file name conflicts). Do you have any advice how I could bypass this behaviour and force the index to be saved in a specific directory? The only 'solution' I can think of is to modify your code, but I would prefer not to do this (besides any copyright/license infringement this might imply and of course, because I don't know if my changes would work as expected). Kind regards from Munich Markus -- Markus Bayerlein Genomatix Software GmbH phone +49 (0)89 599 766 0 Bayerstrasse 85a FAX +49 (0)89 599 766 55 80335 Munich email Germany WWW Legal information: HRB 117956 Amtsgericht Muenchen; Tax-ID: DE 189568720 Geschaeftsfuehrer / Managing Director: Klaus May

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