Syntax issue in INSTALL.py

[JustGitting]

Hi,

I found a small issue in INSTALL.py when installing all workflows/packages:

$ python INSTALL.py core optional fastqc ca ale sga freebayes abyss lap frcbam quast metaphyler eautils ray numpy fcp edena uniprot cython cgal mira matplotlib prokka soap2 masurca kronatools sra glimmer-mg kraken psutil phymm setuptools amos phylosift phmmer phymmbl reapr

During the install I received the following error:

barrnap-0.1/examples/small.fna barrnap-0.1/examples/nohits.fna barrnap-0.1/examples/empty.fna barrnap-0.1/Makefile

Found HMM SCAN /usr/local/bin 3.00 Found prodigal /usr/local/bin Traceback (most recent call last): File "INSTALL.py", line 812, in if float(prodigalVersion) < 2.6: ValueError: could not convert string to float: ^^^^^^^^^^^^^^^^^^^^^^^^^ I double checked if prodigal was working:

$ prodigal -v

Prodigal V2.50: November, 2010

It was, but it's an older version. I fixed the error by changing the following line in the INSTALL.py file:

prodigalVersion = utils.getCommandOutput("%s/prodigal -v 2>&1 | grep -i '^Prodigal V' |sed s/V//g |awk '{printf(\"%%2.2f\n\", $2)}'"%(prodigal), True)

to:

prodigalVersion = utils.getCommandOutput("%s/prodigal -v 2>&1 | grep -i '^Prodigal V' |sed s/V//g |awk '{printf(\"%%2.2f\n\", $2)}'"%(prodigal), True)

it was missing and extra "\" for the new line '\n', which fixed the issue.

Cheers

[skoren]

I think the fix is to change '{printf(\"%%2.2f\n\", $2)}' to '{printf(\"%%2.2f\n\", $2)}' . If so, the INSTALL.py script is fixed and will be commit shortly.

[JustGitting]

Thanks, I edited my post so the double slashes would appear correctly on the revised line. Cheers

[skoren]

Fix committed 1a66de6