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Two bug fixes so dammit can run #245

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Two bug fixes so dammit can run #245

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89e7d2b
pin max version of doit
taylorreiter Aug 22, 2023
e70d579
chase redirect for busco db download
taylorreiter Aug 22, 2023
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6 changes: 3 additions & 3 deletions dammit/tasks/shell.py
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Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,7 @@ def get_download_task(url, target_fn, md5=None, metalink=None):
dict: doit task.
'''

cmd = ['curl', '-o', target_fn]
cmd = ['curl', '-L', '-o', target_fn]
if metalink is not None:
cmd.extend(['--metalink', metalink])
cmd.append(url)
Expand Down Expand Up @@ -147,7 +147,7 @@ def get_download_and_gunzip_task(url, target_fn):
Returns:
dict: doit task.
'''
cmd = 'curl {url} | gunzip -c > {target_fn}'.format(**locals())
cmd = 'curl -L {url} | gunzip -c > {target_fn}'.format(**locals())

name = 'download_and_gunzip:{0}'.format(os.path.basename(target_fn))

Expand Down Expand Up @@ -175,7 +175,7 @@ def get_download_and_untar_task(url, target_dir, label=None):
if label is None:
label = os.path.basename(url)

cmd1 = 'mkdir -p {target_dir}; curl {url} | tar -xz -C {target_dir}'.format(**locals())
cmd1 = 'mkdir -p {target_dir}; curl -L {url} | tar -xz -C {target_dir}'.format(**locals())
name = 'download_and_untar:{0}-{1}'.format(os.path.basename(target_dir), label)
done = os.path.join(target_dir, name) + '.done'
cmd2 = 'touch {done}'.format(done=done)
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2 changes: 1 addition & 1 deletion recipe/meta.yaml
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Expand Up @@ -22,7 +22,7 @@ requirements:
- sphinx_rtd_theme >=0.1.9
- pytest
- pytest-runner
- doit >=0.29.0
- doit >=0.29.0,<0.36.0
- matplotlib
- shmlast

Expand Down