I am attempting to use Galaxy to calculate the mean sequence read
length and identify the range of read lengths for my 454 data. The
data has already been organized and sorted by species. The format of
the data is as follows:
etc...for each species
I have attempted to use the "Summary Statistics" button, however it
appears to only be for numerical data and not sequence data. Is this
User name: dac330
I have a tabular file and using compute (version 1.1.0) tool under text
manipulation menu, I 'm going to do a computation to find rows in which
column2 and 3 (c2 and c3) are similar in values (values are A,T,C and G) .
It seems the syntax for doing that is "c2==c3", but it dosent work. Can
Any help would be appreciated.
We are looking for some advice on going from our current Galaxy to the nglims fork of Galaxy you have created. The last post I've seen on the subject of moving to the nglims Galaxy was here:
Is it still the case that it "would best to first try it out on a separate instance before thinking about integrating with your production Galaxy. It does take a bit of tweaking …." ??
Second, when I install the nglims fork of galaxy is there a way to have galaxy use the tools and genomes in bc-bio? On our original install, before we used bc-bio, I added tools mainly via the tool shed. It would be nice be to have galaxy using the same tools.
Any other advice would be greatly appreciated.
Thank You for your kind reply.
I am having problem in running command in Galaxy.
my current command:
<tool_name> <file_having_multiple_file_name_tab_delimited.txt or .tab>
/usr/bin/x_tool fileList.tab file1.bam file2.bam
I have created xml file so that i can run this command through Galaxy. Its
Can't call method "print" on an undefined value at
/usr/local/share/perl/5.14.2/GTF/tool_x/Calc.pm line 110.
When I am running same command from terminal, its working.
>From these I have hypothesize:
- Galaxy is having different path to run its script, and different file
- FileList.tab contains list of other files which present in same folder.
- As tool is not able to search those files, may be galaxy is having
different path where it run the command.
While uploading file, I am using user defined path so that galaxy will not
create replica of it,
hence when I see error file of Galaxy output (by clicking on (i) symbol )
its showing the same path where all my files are located.
Is there a approved way to configure or otherwise use galaxy to process multiple files with a tool or workflow? Using FASTQ Groomer on dozens of files individually is excruciating.
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Thank You for answers, I am able to learn everyday.
I am having 500 GB hard disk, I am trying to integrate 'x' tool to galaxy
for local lab purpose.
'x' tool require bam files which are of 400 GB file size. When I used Admin
section to upload file my computer hang because of no space.
Is it way that I can tell Galaxy that use these files directly or may be I
can convert files to Galaxy required format so that galaxy will not create
files by itself.
As you can see in my example, I am having 500 GB HDD, and ~400 GB BAM
files, replication of data by Galaxy its not possible for me.
Some option like tell Galaxy about extension and properties of file, so
that it should not replicate.
By command line 'x' is working fine.
Need some really good solution.
Waiting for positive reply.
I'm trying to run the attached workflow to run tophat followed by cuffdiff. But when I hit run a message saying server error appears and that is all (see screen shot attached). I have not clue where the error can be. It appear a very simple work flow.
I will appreciate if someone give an idea of what can be wrong.
Hallo Galaxy users,
I would like to annotate variants (in vcf file) found in my bacterial
genomes and look which of them cause non-synonymous mutations. I have
found two tools in the Main Galaxy that I can use for this purpose
(snpEff and Annovar), but I have problems with them.
How can I change the input genome in snpEff? The only available choice
in C. elegans. How can I choose my genome, already uploaded in my history?
Regarding Annovar, which file formats are required as Gene annotations/
Annotation Regions/ Annotation Databases? Reading the tool manual, it
seems I can create my own txt/tabular files and use them for annotation,
but the tool in Galaxy doesn't allow me to select any file, even if I
have txt files in my history.
Any other suggested tool I can use?