Question: Bam File error uploading
0
gravatar for shambyross
15 months ago by
shambyross10
shambyross10 wrote:

Hello,

I am new to galaxy and any data analysis. After uploading bam files into galaxy I get the error (see below). Can you help me to resolve this issue? I do use root before going into galaxy. Thanks,

Ross

Traceback (most recent call last): File "/private/var/root/galaxy/tools/data_source/upload.py", line 431, in <module> __main__() File "/private/var/root/galaxy/tools/data_source/upload.py", line 420, in __main__ add_file( dataset, registry, json_file, output_path ) File "/private/var/root/galaxy/tools/data_source/upload.py", line 347, in add_file if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): File "/private/var/root/galaxy/lib/galaxy/datatypes/binary.py", line 218, in dataset_content_needs_grooming version = self._get_samtools_version() File "/private/var/root/galaxy/lib/galaxy/datatypes/binary.py", line 181, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 711, in __init__ errread, errwrite) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1343, in _execute_child raise child_exception OSError: [Errno 13] Permission denied

upload path admin error samtools • 682 views
ADD COMMENTlink modified 14 months ago by y.hoogstrate450 • written 15 months ago by shambyross10
1
gravatar for y.hoogstrate
15 months ago by
y.hoogstrate450
Netherlands
y.hoogstrate450 wrote:

I think it can't find samtools after all. Could you copy paste what happens if you type:

command -v samtools

and

which -a samtools

those commands should look for samtools in the defined PATHs. If it does not return a path, e.g. /usr/local/bin/samtools, samtools is not available for galaxy (which does not mean samtools is not present on your system). If it is not present, please try the follow:

  • find the directory in which samtools is present - somewhere like /../../../samtools/mimodd_bins/bin I suppose?
  • before running galaxy, run: export PATH="$PATH:/../../../samtools/mimodd_bins/bin" to add samtools to the directories in which the computer should be looking for samtools. Don't switch terminal, this variable is lost after closing the session
  • confirm it works with the which -a and command -v commands above
  • try galaxy
  • if it works, make the solution permenent by copying the entire export command into a config file / shell script that automatically runs after starting up a terminal. It may sounds vague an generic but I don't know which files are executed at commandline startup on a Mac. On linux this could be ~/.bashrc or ~/.zshrc or ~/.profile.
ADD COMMENTlink written 15 months ago by y.hoogstrate450

Hello hoogstrate,

Sorry for not responding. So I ran the commands you have suggested it. Since samtools were not available for galaxy i ran as suggested by the EXPORT command however it has been 30 minutes since i ran this command. How long does it take to get output and will I get output. I know directory for samtools exists on my computer - found it.

Can you suggest any other issues that might be preventing galaxy from seeing samtools.

Thank you,

Ross

ADD REPLYlink written 15 months ago by shambyross10
0
gravatar for Jennifer Hillman Jackson
15 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Was Samtools installed from the Tool Shed with dependencies included? The upload tool requires this tool package. Also install Picard as a default tool (utilized by many other tools/functions). Or, if Samtools/Picard are already installed on your server, make sure both are in the PATH Galaxy uses, Galaxy has permissions to use the binaries, and that the versions are the most current (same as in the tool shed).

After that is confirmed, if the BAM file is over 2 GB, use FTP upload or load the data from the local file system into a data library (where it can be moved into a history for analysis).

Thanks, Jen, Galaxy team

ADD COMMENTlink written 15 months ago by Jennifer Hillman Jackson23k
0
gravatar for shambyross
15 months ago by
shambyross10
shambyross10 wrote:

I have downloaded MiModD and it was stated samtools and bcftools were included.

I will try what you have suggested.

Thanks

ADD COMMENTlink written 15 months ago by shambyross10

It could be that your samtools does not have the execute bit set for the galaxy user. Could you try this on commandline: sudo chmod 755 $(which samtools)

ADD REPLYlink modified 15 months ago • written 15 months ago by y.hoogstrate450

I finally worked out just by updating galaxy. thank you@

Now i am trying to set up my tracker when I try to view alignment is gives me an error that bedtools comman not found and /ust/local/bin/bedGraphToBigWig: permission denied.

Can you suggest how I might fix these issues? thank you

ADD REPLYlink written 14 months ago by shambyross10

Obviously the same problem: sudo chmod 755 $(which bedGraphToBigWig) or even better: sudo chmod -R 755 /usr/local/bin

ADD REPLYlink written 14 months ago by y.hoogstrate450

Sorry for bugging you so much,

I have downloaded bowtie2 on toolshed and it states "installed missing tool dependencies". Can you explain to me what it means and how to fix it?

Thank you again,

Ross

ADD REPLYlink written 14 months ago by shambyross10
0
gravatar for shambyross
15 months ago by
shambyross10
shambyross10 wrote:

Hi y.hoogstrate,

I have typed into the terminal as you suggested and got the following:

Rosss-MacBook-Pro:~ root# sudo chmod 755 $(which samtoools) usage: chmod [-fhv] [-R [-H | -L | -P]] [-a | +a | =a [i][# [ n]]] mode|entry file ... chmod [-fhv] [-R [-H | -L | -P]] [-E | -C | -N | -i | -I] file ...

I am novice to a computer coding - can you suggest what i should do next?

Ross

ADD COMMENTlink written 15 months ago by shambyross10
0
gravatar for shambyross
14 months ago by
shambyross10
shambyross10 wrote:

Hi hoogstrata,

when I type in terminal chmod 755$ (which bcftools)

I get the following

usage: chmod [-fhv] [-R [-H | -L | -P]] [-a | +a | =a [i][# [ n]]] mode|entry file ... chmod [-fhv] [-R [-H | -L | -P]] [-E | -C | -N | -i | -I] file ...

I have tried your suggestion with :

sudo chmod -R 755 /usr/local/bin

ADD COMMENTlink written 14 months ago by shambyross10
0
gravatar for y.hoogstrate
14 months ago by
y.hoogstrate450
Netherlands
y.hoogstrate450 wrote:

I think this is very trivial knowledge and really necessary to be able to host a galaxy server and I would recommend you to some kind of crash course on the linux system, e.g. http://web.csc.fi/english/csc/courses/archive/material/svali2011/UnixCrash

ADD COMMENTlink written 14 months ago by y.hoogstrate450
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