From 89e7d2b11123df7854ac4c0e73524728e2ef5d1a Mon Sep 17 00:00:00 2001 From: Taylor Reiter Date: Tue, 22 Aug 2023 14:51:17 -0400 Subject: [PATCH 1/2] pin max version of doit --- recipe/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipe/meta.yaml b/recipe/meta.yaml index f75a32b1..a3083084 100644 --- a/recipe/meta.yaml +++ b/recipe/meta.yaml @@ -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 From e70d5798fdae678142f19be78a449885f14c63d9 Mon Sep 17 00:00:00 2001 From: Taylor Reiter Date: Tue, 22 Aug 2023 14:51:35 -0400 Subject: [PATCH 2/2] chase redirect for busco db download --- dammit/tasks/shell.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/dammit/tasks/shell.py b/dammit/tasks/shell.py index 613dd39b..9111c146 100644 --- a/dammit/tasks/shell.py +++ b/dammit/tasks/shell.py @@ -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) @@ -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)) @@ -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)