Galaxy itself needs samtools, and this is not handled via the Tool Shed which only does dependencies of Galaxy Tools. I don't think the website is clear enough about this, https://wiki.galaxyproject.org/Admin/GetGalaxy just points at https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies Which version of Galaxy are you using? Older versions had to have an older samtools (which had a different API for using samtools sort). Peter On Mon, Dec 5, 2016 at 12:36 PM, Konstantinos Voutetakis <kvoutet@eie.gr> wrote:

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 ------------------------------ ---------------------------------------------------- tel.: +30-210-7273894 e-mail: kvoutet@eie.gr

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