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berman-lab / ymap

YMAP - Yeast Mapping Analysis Pipeline : An online pipeline for the analysis of yeast genomic datasets.
MIT License
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FASTQC current version change #63

Closed darrenabbey closed 7 years ago

darrenabbey commented 7 years ago

While installing Ymap on my home system, I ran into an issue with the currently available version of FASTQC (v0.11.5). The program generates all of its files into a contained directory as before, but most of those files are now generated within a ZIP archive. This makes a text file which contains the FASTQ coding format inaccessible to the shell scripts which need it (for running GATK functions).

Adding the apparently new "--extract" option to each call of FASTQC resolved this issue for me. This change would need to be done in: [Ymap_root]/scripts_seqModules/scripts_WGseq/project.paired_WGseq.install_3.sh [Ymap_root]/scripts_seqModules/scripts_WGseq/project.single_WGseq.install_3.sh [Ymap_root]/scripts_seqModules/scripts_ddRADseq/project.paired_ddRADseq.install_3.sh [Ymap_root]/scripts_seqModules/scripts_ddRADseq/project.single_ddRADseq.install_3.sh [Ymap_root]/scripts_seqModules/scripts_IonExpressSeq/project.paired_IonExpressSeq.install_3.sh [Ymap_root]/scripts_seqModules/scripts_IonExpressSeq/project.single_IonExpressSeq.install_3.sh [Ymap_root]/scripts_seqModules/scripts_RNAseq/project.paired_RNAseq.install_3.sh [Ymap_root]/scripts_seqModules/scripts_RNAseq/project.single_RNAseq.install_3.sh

The specific lines can be found by searching for "fastqc".

vladimirg commented 7 years ago

The versions of all 3rd parties must be follow strictly using the Setting up Ymap locally guide. Anything else is unsupported.

darrenabbey commented 7 years ago

Older versions if FASTQC don't appear to be available. -d

On Dec 10, 2016 2:07 AM, "Vladimir Gritsenko" notifications@github.com wrote:

The versions of all 3rd parties must be follow strictly using the Setting up Ymap locally https://github.com/berman-lab/ymap/wiki/Setting-up-Ymap-locally guide. Anything else is unsupported.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/berman-lab/ymap/issues/63#issuecomment-266189012, or mute the thread https://github.com/notifications/unsubscribe-auth/AKPuRNcOiY5HP2dWHRUTB0Diu9i-iyVSks5rGl3LgaJpZM4LJl3R .

vladimirg commented 7 years ago

They're available, but hidden (don't know why). I've added the link for the Linux version to the installation guide. We actually should have added it sooner - thanks for catching this!

darrenabbey commented 7 years ago

Thanks! I had looked for it a few times and then shrugged and moved on.

On Dec 10, 2016 3:30 AM, "Vladimir Gritsenko" notifications@github.com wrote:

They're available, but hidden (don't know why). I've added the link for the Linux version to the installation guide. We actually should have added it sooner - thanks for catching this!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/berman-lab/ymap/issues/63#issuecomment-266192258, or mute the thread https://github.com/notifications/unsubscribe-auth/AKPuREiJj-3r9urBmrYDxvfZu4VQ_FAyks5rGnFSgaJpZM4LJl3R .