Hi Dannon,
Thanks for the reply. Sorry for the duplicate. I was wondering that the original subject sounded like a user problem so I updated it...
Actually we are having a little down time right now for a file system check. I'll try your suggestions asap and let you know. At the mean time, could you please elaborate this a little bit? I noticed that in the tool_conf.xml, not every tool is shown on the panel although they are all defined there in the same format. I also noticed that all the tool xml files, such as
<section id="samtools" name="NGS: SAM Tools">
<tool file="samtools/sam_bitwise_flag_filter.xml" />
<tool file="samtools/sam2interval.xml" />
<tool file="samtools/sam_to_bam.xml" />
<tool file="samtools/bam_to_sam.xml" />
<tool file="samtools/sam_merge.xml" />
<tool file="samtools/samtools_mpileup.xml" />
<tool file="samtools/sam_pileup.xml" />
<tool file="samtools/pileup_parser.xml" />
<tool file="samtools/pileup_interval.xml" />
<tool file="samtools/samtools_flagstat.xml" />
<tool file="samtools/samtools_rmdup.xml" />
<tool file="samtools/samtools_slice_bam.xml" />
</section>
the directory samtools and all these xml files are no longer in the tools directory. seems that upgrade deleted them. is this correct? or they are moved to somewhere else? I looked around but didn't see.
Based on this, I think that even I removed the tool_panel.xml file you mentioned, I will still not be able to restore samtools even I could see it...could you please let me know how I could configure this?
Thanks,
Rui