Dear Sir(s),
I have consumed a few days in order to resolve this issue but nothing! I
have installed all the SAM tools of public Galaxy in my local galaxy via
the Toolshed (installing automatically all the dependencies were needed). I
have also export the path of the executable file SAMtools from bin folder
to my Galaxy path and I take the following error during uploading:
Traceback (most recent call last):
File "/home/user/galaxy/tools/data_source/upload.py", line 434, in <module>
__main__()
File "/home/user/galaxy/tools/data_source/upload.py", line 423, in __main__
add_file( dataset, registry, json_file, output_path )
File "/home/user/galaxy/tools/data_source/upload.py", line 317, in add_file
if datatype.dataset_content_needs_grooming( dataset.path ):
File "/home/user/galaxy/lib/galaxy/datatypes/binary.py", line 251,
in dataset_content_needs_grooming
version = self._get_samtools_version()
File "/home/user/galaxy/lib/galaxy/datatypes/binary.py", line 212,
in _get_samtools_version
raise Exception(message)
Exception: Attempting to use functionality requiring samtools, but it
cannot be located on Galaxy's PATH.
When I am in my galaxy folder (from where I connect to my galaxy server)
and I type samtools in the terminal I take:
Program: samtools (Tools for alignments in the SAM format)
Version: 0.1.19-44428cd
Usage: samtools <command> [options]
Command: view SAM<->BAM conversion
sort sort alignment file
mpileup multi-way pileup
depth compute the depth
faidx index/extract FASTA
tview text alignment viewer
index index alignment
idxstats BAM index stats (r595 or later)
fixmate fix mate information
flagstat simple stats
calmd recalculate MD/NM tags and '=' bases
merge merge sorted alignments
rmdup remove PCR duplicates
reheader replace BAM header
cat concatenate BAMs
bedcov read depth per BED region
targetcut cut fosmid regions (for fosmid pool only)
phase phase heterozygotes
bamshuf shuffle and group alignments by name
What can I do? I installed galaxy to my pc (ubuntu 16.04) before two weeks
and it is up to date. I would be grateful for your help.
Yours sincerely,
Kostas
--
Konstantinos G. Voutetakis, MSc - Research Officer
National Hellenic Research Foundation (N.H.R.F.)
Institute of Biology, Medicinal Chemistry and Biotechnology
48 Vas. Constantinou Ave., Athens 11635
Greece
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tel.: +30-210-7273894 <%2B30-210-7273752>
e-mail: kvoutet(a)eie.gr