[Debian-med-packaging] Bug#756296: fastqc: Fastq cann't find configuration files

[Alexey Sergushichev]

Package: fastqc
Version: 0.11.2+dfsg-1
Severity: important

Dear Maintainer,

fastqc can't find configuraion files which mak it not working.

For example, if I have a simple file test.fastq:

@test
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+test
IHGFEDCBA@?>=<;:9876543210/.-,+*)(\'&%$#

and run fastqc test.fastq I get these errors:

java.io.FileNotFoundException: cannot find Confituration/adapter_list.txt
	at uk.ac.babraham.FastQC.Modules.AdapterContent.<init>(AdapterContent.java:79)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:129)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.<init>(OfflineRunner.java:95)
	at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:308)
Started analysis of test.fastq
Analysis complete for test.fastq
Failed to process file test.fastq
java.lang.IllegalArgumentException: input == null!
	at javax.imageio.ImageIO.read(ImageIO.java:1388)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:377)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:301)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:163)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:110)
	at java.lang.Thread.run(Thread.java:744)

In the upstream version (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.2.zip)
running ./fastqc works perfectly fine, probably because it has
Configuration directory in in the same directory as the perl script.

-- System Information:
Debian Release: 7.6
  APT prefers stable
  APT policy: (700, 'stable'), (699, 'testing'), (600, 'unstable'), (500, 'oldstable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 3.14-1-amd64 (SMP w/4 CPU cores)
Locale: LANG=ru_RU.UTF-8, LC_CTYPE=ru_RU.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash

Versions of packages fastqc depends on:
ii  libcommons-math3-java  3.3-1
ii  libjbzip2-java         0.9.1-3
ii  libsam-java            1.46-1

fastqc recommends no packages.

fastqc suggests no packages.

-- no debconf information