From 2835637a95e801648cf3a1dcb393875137e103fe Mon Sep 17 00:00:00 2001 From: Riccardo Murri Date: Mon, 14 Nov 2016 23:49:42 +0100 Subject: [PATCH] Correct solution to Ex. 4.B to with with `blastp` instead of `blastpgp`. --- docs/programmers/tutorials/workflows/solutions/ex4b.py | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/docs/programmers/tutorials/workflows/solutions/ex4b.py b/docs/programmers/tutorials/workflows/solutions/ex4b.py index 327a1ac7..27331431 100755 --- a/docs/programmers/tutorials/workflows/solutions/ex4b.py +++ b/docs/programmers/tutorials/workflows/solutions/ex4b.py @@ -62,7 +62,7 @@ def new_tasks(self, extra): return apps_to_run -from gc3libs.quantity import GB +from gc3libs.quantity import GB, minutes class BlastApp(Application): """Run BLAST on two files.""" @@ -71,10 +71,8 @@ def __init__(self, input1, input2, e_value, output_fmt): inp2 = basename(input2) Application.__init__( self, - # NOTE: does not work as written! BLAST+ is required - # to compare two FASTA files - arguments=["blastpgp", "-i", inp1, "-d", inp2, - "-e", e_value, "-m", output_fmt, "-o", "output.txt"], + arguments=["blastp", "-query", inp1, "-subject", inp2, + "-evalue", e_value, "-outfmt", output_fmt, "-out", "output.txt"], inputs=[input1, input2], outputs=["output.txt"], output_dir=("blast-" + inp1 + "-" + inp2 + ".d"),