fix bug in handling multiple --single_url files

[levinas]

There seem multiple bugs when multiple SE files are supplied as URLs.

The following commands fail:

1. Implicit auto recipe

$ ar-run --single_url https://edwards.sdsu.edu/~redwards/ED252/252cat.fasta --single_url https://edwards.sdsu.edu/~redwards/ED252/2.GAC.454Reads.fastq

2. Explicit auto

$ ar-run --single_url https://edwards.sdsu.edu/~redwards/ED252/252cat.fasta --single_url https://edwards.sdsu.edu/~redwards/ED252/2.GAC.454Reads.fastq -r auto

3. When one of the assemblers doesn't support the data

$ ar-run --single_url https://edwards.sdsu.edu/~redwards/ED252/252cat.fasta --single_url https://edwards.sdsu.edu/~redwards/ED252/2.GAC.454Reads.fastq -a velvet idba spades In this case, idba fails and prevents spades from being run. Even though velvet completed successfully, the report is empty.

This one succeeds:

4. When all the assemblers support the data

$ ar-run --single_url https://edwards.sdsu.edu/~redwards/ED252/252cat.fasta --single_url https://edwards.sdsu.edu/~redwards/ED252/2.GAC.454Reads.fastq -a velvet spades

[levinas]

Update:

1 and 2 seem the result of server/client version mismatch on elm. I redeployed server v0.5.4 on elm.

Need to verify 3 on the kbase production server.

[cbun]

The modules aren't failing silently. Fails with single-end + idba too.

[cbun]

1be1aca51727a0d60465ef76b12a95a0eb3b4bdc