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crs4 / hadoop-galaxy

Light Hadoop-Galaxy integration
BSD 3-Clause "New" or "Revised" License
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make_pathset doesn't work with multiple paths in its text box #1

Open ilveroluca opened 10 years ago

ilveroluca commented 10 years ago

If one tries to provide the make_pathset tool with multiple paths through the galaxy interface the output isn't as expected.

For instance, inserting the local paths /home/pireddu/data/100_r1.fastq /home/pireddu/data/100_r2.fastq in the text box results in this error:

ls: Cannot access file:///home/pireddu/data/100_r1.fastq /home/pireddu/data/100_r2.fastq: No such file or directory.
Could not list datapath file:///home/pireddu/data/100_r1.fastq /home/pireddu/data/100_r2.fastq.  Please check whether it exists
Message: Command '['/home/pireddu/Programs/hadoop-1.2.1/bin/hadoop', 'dfs', '-ls', 'file:///home/pireddu/data/100_r1.fastq /home/pireddu/data/100_r2.fastq']' returned non-zero exit status 255

The tool is evidently interpreting the entire contents of the text box as a single path (I think it's because of the quotes around the parameter in the tool's galaxy wrapper.