From 006a2431ef64785f4c0bde36f3494b824d461feb Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Wed, 20 Mar 2019 16:42:20 +0100 Subject: [PATCH 1/3] download: Make unzipped files executable. Fixes nf-core/tools#289 --- nf_core/download.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/nf_core/download.py b/nf_core/download.py index 2fb472b00d..176f2ba159 100644 --- a/nf_core/download.py +++ b/nf_core/download.py @@ -170,6 +170,11 @@ def download_wf_files(self): gh_name = '{}-{}'.format(self.wf_name, self.wf_sha).split('/')[-1] os.rename(os.path.join(self.outdir, gh_name), os.path.join(self.outdir, 'workflow')) + # Make downloaded files executable + for dirpath, subdirs, filelist in os.walk(os.path.join(self.outdir, 'workflow')): + for fname in filelist: + os.chmod(os.path.join(dirpath, fname), 0o775) + def find_container_images(self): """ Find container image names for workflow """ From c058158e407fbc4e17f4f3e780d93b163adac7c9 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Wed, 20 Mar 2019 16:43:19 +0100 Subject: [PATCH 2/3] Changelog --- CHANGELOG.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 52b1e45faf..d8e135fdc2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,7 +8,9 @@ #### Tools helper code * Drop [nf-core/rnaseq](https://github.com/nf-core/rnaseq]) from `blacklist.json` to make template sync available -* Fix bug in `nf-core download` so that it now fetches the latest release by default +* Fix bugs in `nf-core download` + * The _latest_ release is now fetched by default if not specified + * Downloaded pipeline files are now properly executable ## [v1.5](https://github.com/nf-core/tools/releases/tag/1.5) - 2019-03-13 Iron Shark From 30ebd9ed6002e495d9c2d58808779a5f44f25823 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Mon, 25 Mar 2019 14:10:46 +0100 Subject: [PATCH 3/3] Markdown: fix list indentation --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d8e135fdc2..dc43547fa0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,8 +9,8 @@ #### Tools helper code * Drop [nf-core/rnaseq](https://github.com/nf-core/rnaseq]) from `blacklist.json` to make template sync available * Fix bugs in `nf-core download` - * The _latest_ release is now fetched by default if not specified - * Downloaded pipeline files are now properly executable + * The _latest_ release is now fetched by default if not specified + * Downloaded pipeline files are now properly executable ## [v1.5](https://github.com/nf-core/tools/releases/tag/1.5) - 2019-03-13 Iron Shark