[galaxy-dev] Error while running Cuffdiff
Dear Galaxy development team, I am trying to analyze RNAseq data using the following pipeline: FASTQ Trimmer | HISAT | Cufflinks | Cuffmerge | Cuffdiff | CummeRbund I am able to run everything without a problem up to the CuffDiff step. I always get an error message. I sent a bug report and posted on Biostars-Galaxy. Jen replied to my comment on Biostars and recommended I email galaxy-dev. Please see the details of the error message here: https://biostar.usegalaxy.org/p/18331/ I think it may have a problem loading the SQlite database? Even though CuffDiff gives an error message, I was still able to download the data from CuffDiff in tabular format and perform some data analysis using R. However, it would be useful to be able to use cummeRbund to analyze the cuffdiff data. Thank you in advance for all your help. Let me know if there is any other information I can provide to clarify the error, etc. Best Regards, Ravi ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] question using PICRUSt COG vs. KEGG
Hello, I have a general question. A metagenome prediction in PICRUSt worked fine when I ran it requesting KEGG output (running on MAIN), but I got the below error when requesting COG output. I could not find in the on-line forums or other areas of support what may be needed regarding a different input file or change in the normalization by copy number in order to get COG instead of KEGG output? Thank you very much for your help! Ana Traceback (most recent call last): File "/n/galaxy/www/galaxy_hutlab14/galaxy-hutlab14-20150109/tools/picrust_galaxy/scripts/predict_metagenomes.py", line 337, in main() File "/n/galaxy/www/galaxy_hutlab14/galaxy-hutlab14-20150109/tools/picrust_galaxy/scripts/predict_metagenomes.py", line 171, in main ids_to_load=ids_to_load,verbose=opts.verbose,transpose=True) File "/n/galaxy/www/galaxy_hutlab14/galaxy-hutlab14-20150109/tools/picrust_galaxy/scripts/predict_metagenomes.py", line 113, in load_data_table genome_table_fh = gzip.open(data_table_fp,'rb') File "/n/hutlab11/tools/python2.7.8/lib/python2.7/gzip.py", line 34, in open return GzipFile(filename, mode, compresslevel) File "/n/hutlab11/tools/python2.7.8/lib/python2.7/gzip.py", line 94, in __init__ fileobj = self.myfileobj = __builtin__.open(filename, mode or 'rb') IOError: [Errno 2] No such file or directory: '/usr/local/galaxy-python/lib/python2.7/site-packages/picrust/data/cog_13_5_precalculated.tab.gz' ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Using operations on multiple datasets
In addition to Bjoern’s response, tools written to take a single input like this: will automatically accept a dataset collection, both in workflows and in the tool form UI. > On Jul 5, 2016, at 5:25 PM, Björn Grüning wrote: > > Hi, > > Am 05.07.2016 um 23:18 schrieb D K: >> Sorry for the crosspost to Biostars, but I didn't get a response, so I >> thought I'd post here: >> >> I just noticed that Galaxy allows creation of lists of datasets by clicking >> on the "Operations on multiple datasets" in the history panel. How does one >> use this with a custom tool (e.g. what does one put between the >> tags). Is the list treated as a text file with a list of each >> file? I couldn't find any examples or documentation online. I'd appreciate >> it if someone could point me in the right direction. > > You can not use this feature in a tool, it's pure UI. But you can use > multiple="True" > > https://github.com/galaxyproject/tools-iuc/blob/180a403421967d36f995941b1a4561349d75cfc5/tools/mothur/merge.files.xml#L32 > > maybe this helps? > Cheers, > Bjoern > >> Thanks! >> >> >> >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
