Skip to content
GitLab
Menu
Projects
Groups
Snippets
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Rayan CHIKHI
serratus-batch-dl
Commits
6905947c
Commit
6905947c
authored
Jun 17, 2020
by
Rayan CHIKHI
Browse files
oops, parallel-fastq-dump is maybe using /tmp
parent
896fc987
Changes
1
Hide whitespace changes
Inline
Side-by-side
src/batch_processor.py
View file @
6905947c
...
...
@@ -45,7 +45,8 @@ def process_file(accession, region):
# download reads from accession
os
.
system
(
'mkdir -p out/'
)
os
.
system
(
'prefetch '
+
accession
)
os
.
system
(
'/parallel-fastq-dump --split-files --outdir out/ --threads 4 --sra-id '
+
accession
)
os
.
system
(
'mkdir -p tmp/'
)
os
.
system
(
'/parallel-fastq-dump --split-files --outdir out/ --tmpdir tmp/ --threads 4 --sra-id '
+
accession
)
files
=
os
.
listdir
(
os
.
getcwd
()
+
"/out/"
)
print
(
"after fastq-dump, dir listing of out/"
,
files
)
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment