Hi Rui,
This error probably means that the binaries from UCSC are not installed
or the path to the tools is incorrect. "ucsc_tools" is a package
requirement for the tools that use these binaries in the .xml portion of
the wrapper (for those in the dist/devteam).
If you are running your own instance, without any dependencies on other
institutional resources or repositories, then any binaries needed should
in most cases come from UCSC in the Downloads area under source and be
installed. Some wrappers are in the distribution (such as wigToBigWig in
galaxy-dist / tools / filters ), but there are others are in the tool shed.
http://hgdownload.cse.ucsc.edu/admin/exe
http://usegalaxy.org/toolshed
Where the other repo comes in, I am not sure. Maybe from a wrapper
installed from the Tool Shed (or another source) that needs a UCSC
binary. If it is dependent on a particular version, that could be a
reason for a distinct repo. Contacting the wrapper author may help to
clarify. Tools in the distribution and from "devteam" in the Tool Shed
all use the standard UCSC source to my knowledge.
Maybe others will add in comments to this thread, if they recognize
this. Or, your sysadmin can help if you contact them, if there shared
resources to make use of.
On 1/15/14 10:30 AM, ruiwang.sz wrote:
Hi Jennifer,
Thanks for the note.
A related question, do we have a 'ucsc_tool'? I sometimes saw the
warning of failed dependency on ucsc_tool, but I'm not sure what it
is. I found that there are many binary/script utilities:
https://github.com/adamlabadorf/ucsc_tools
should I install all these by running
python setup.py install
or I could just copy all those executables to my own utility dir?
Thanks,
Rui
On Wed, Jan 15, 2014 at 7:51 AM, Jennifer Jackson <[email protected]
<mailto:[email protected]>> wrote:
Hello Rui,
The problems you are describing have to do with the format of the
input wig dataset.
It looks as if you have corrected the chromosome names to be
identical to the reference genome build used (required). There are
options to overcome the other issues:
1. verify that your data has no browser lines, and has track and
definition lines in the correct format. UCSC is the definitive
source for this info, as both the underlying tool and this format
were developed by them. Links to their information and the general
format rules in Galaxy can be found here
https://wiki.galaxyproject.org/Learn/Datatypes#Wig_and_bigWig
2. send only a single wig file to the tool at a time, when using
the Galaxy wrapper.
3. use the 'full parameter' option 'Clip chromosome positions:' to
removing overhanging coordinates (known to be produced by several
common tools). This is after confirming that the build is correct
- overhanging coordinates can be a clue that there is a genome
mismatch problem.
https://wiki.galaxyproject.org/Support#Reference_genomes
4. note that variable step data comes in two formats fixed and
variable - and that variable has two format versions, those with a
a span definition and those without (see examples in wig examples
in #1). I have only seen this tool run successfully, in Galaxy, on
the type without "span" included. If you find that the span
variable is problematic after correcting any other format issue
issues, switch to the format without span.
Good luck,
Jen
Galaxy team
On 1/14/14 9:52 PM, ruiwang.sz <http://ruiwang.sz> wrote:
Hi All,
I'm having an error at this:
*Dataset 18: Wig/BedGraph-to-bigWig on data 12*
Tool execution generated the following error message:
grep: writing output: Broken pipe
grep: writing output: Broken pipe
grep: writing output: Broken pipe
grep: writing output: Broken pipe
..
put: Broken pipe
grep: writing output: Broken pipe
grep: writing output: Broken pipe
..
grep: writing output: Broken pipe
grep: write error
Error running wigToBigWig.
The tool produced the following additional output:
hashMustFindVal: '1' not found
I searched and found this link:
http://redmine.soe.ucsc.edu/forum/index.php?t=msg&goto=10745&S=2a335135e76cf9b7160c0e9d41353767
which says that there is a naming convention difference.
I followed what he did and replaced chrom=1 to chrom=chr1 etc,
now it goes further, but
still dies with error:
line 18020168 of /tmp/t3: chromosome chr1 has 195276750 bases,
but item ends at 195276760
line 18020169 of /tmp/t3: chromosome chr1 has 195276750 bases,
but item ends at 195276770
line 18020170 of /tmp/t3: chromosome chr1 has 195276750 bases,
but item ends at 195276780
line 18020171 of /tmp/t3: chromosome chr1 has 195276750 bases,
but item ends at 195276790
line 18020172 of /tmp/t3: chromosome chr1 has 195276750 bases,
but item ends at 195276800
line 18020173 of /tmp/t3: chromosome chr1 has 195276750 bases,
but item ends at 195276810
line 18020174 of /tmp/t3: chromosome chr1 has 195276750 bases,
but item ends at 195276820
line 18020175 of /tmp/t3: chromosome chr1 has 195276750 bases,
but item ends at 195276830
line 18020176 of /tmp/t3: chromosome chr1 has 195276750 bases,
but item ends at 195276840
line 18020177 of /tmp/t3: chromosome chr1 has 195276750 bases,
but item ends at 195276850
line 18020178 of /tmp/t3: chromosome chr1 has 195276750 bases,
but item ends at 195276860
line 18020179 of /tmp/t3: chromosome chr1 has 195276750 bases,
but item ends at 195276870
line 18020180 of /tmp/t3: chromosome chr1 has 195276750 bases,
but item ends at 195276880
Unrecognized line 18020181 of /tmp/t3:
variableStep chr10 span=10
Error running wigToBigWig.
The command line is: wigToBigWig /tmp/t3
/home/bioinfoadmin/app/galaxy-dist/tool-data/shared/ucsc/chrom/ucsc_gg4.len
/home/bioinfoadmin/app/galaxy-dist/database/files/000/dataset_769.dat
-clip 2>&1 || echo "Error running wigToBigWig." >&2
Quite puzzled...wondering if anyone has seen it before and could
give me a hand. :-) I'll really appreciate!
Thanks,
Rui
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--
Jennifer Hillman-Jackson
http://galaxyproject.org
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Jennifer Hillman-Jackson
http://galaxyproject.org
___________________________________________________________
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