Question: spades assembler in local Galaxy on MacOSX
0
gravatar for cgibas
3.8 years ago by
cgibas20
United States
cgibas20 wrote:

I'm looking to see if there is any feasible way to set up and run a small assembly problem on a local Galaxy instance using tools downloaded from the Tool Shed, as an exercise for students. I installed the SPAdes assembler knowing that I've run it successfully on the machine I'm using, on the chosen data set, and in a reasonable time.  When I go to run it, however, I get this error:


== Error ==  It looks like you are using SPAdes binaries for another platform.
You can obtain SPAdes binaries in one of two ways:
1. Download them from http://bioinf.spbau.ru/content/spades-download
2. Build source code with ./spades_compile.sh script

In case you have troubles running SPAdes, you can write to spades.support@bioinf.spbau.ru
Please provide us with params.txt and spades.log files from the output directory.
Failed with code 256
Command spades.py --disable-gzip-output --careful -t 1 -k 21,33,55,77,99,127 --pe1-fr --pe1-s fastq:/Users/cgibas/galaxy-dist/database/files/000/dataset_334.dat -o output_dir
Message: 256

...so either the tool authors didn't anticipate that it might be installed on an OSX system or the installer didn't perceive my system correctly.  I've had similar problems with some of the other tools -- they appear to install correctly but then they error out when run.

Is there another place I should be getting tools from, other than the main Tool Shed, when I'm working on MacOSX?  Thanks.

assemblers tool shed local • 2.3k views
ADD COMMENTlink modified 3.8 years ago by Jennifer Hillman Jackson25k • written 3.8 years ago by cgibas20
1
gravatar for Jennifer Hillman Jackson
3.8 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

It may be that the binaries associated with a tool are assuming a linux environment (not checking specifically, or are grabbing pre-compiled binaries, not actually compiling them for a specific system). But you can download/install or use binaries for MaxOS, even those you already have on your system, as long as the versions are in agreement. Some testing to ensure compatibility may be necessary.

The tool author (authors) can always be contacted, through the Tool Shed, to let them know about what is going on. Would be nicer of course if tools recognized the platform properly and installed to suit.

For this tool, the link to the source is almost correct in the message you shared .. this is it: http://bioinf.spbau.ru/en/content/spades-download-0 If you have it on your computer still (you mentioned it worked there before?) - just use that binary - no need to have two copies. 

Hopefully this helps, Jen, Galaxy team

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by Jennifer Hillman Jackson25k
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