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Add register_docker, --force and ENV vars for defaults #6

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Add register_docker, --force and ENV vars for defaults #6

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juanesarango
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@juanesarango juanesarango commented Feb 7, 2024 •
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Add:

  • register_docker: to create docker scripts as executables
  • --force: to force overwriting existing targets
  • ENV vars to configure the default values for --bindir, --optdir, --tmpvar and --volumes.

Checklist:

  • 🐛   Bug fix
  • 🚀   New feature
  • 🔧   Code refactor
  • ⚠️   Breaking change that would cause existing functionality to change
  • 📘   I have updated the documentation accordingly
  • ✅   I have added tests to cover my changes

@juanesarango
🔧 add default config via ENV vars
8d0846b
@juanesarango
🐛 fix unused option and update click version
f335c10
@juanesarango
🐛 fix ENV var names
7b1c46a
@juanesarango
📒 add epilogue to --help about env vars
4291119
@juanesarango
🔧 remove epilog
543fe53
@juanesarango
🐋 add register_docker
88d2d51
@juanesarango
✅ add tests for register_docker
610b84c
@juanesarango
✅ fix error in docker command
0634ac8
@juanesarango
✅ fix $TMP and add --force
e9399a2
@juanesarango
✅ upgrade ubuntu version in Dockerfile
de57678
@juanesarango
✅ use public repos for tests
8f96e49
@juanesarango
🐛 fix extrypoint conditional
2c80432
@juanesarango
👥 run docker with same uid and gid
b53bdc2
@juanesarango
📦 use first available .sif singularity local image
1eacb0f
@juanesarango
🪖 force to use .sif singularity image when multiple
54f3b25
@juanesarango
🔧 add --virtualenvwrapper option
2794d72
@juanesarango
📦 add --container option to register_toil
b4644e9
@juanesarango
🔧 add docker:// to image_url when using singularity
99beb2a
@juanesarango
🔧 fix image_url
f45e9b7
@juanesarango
🐛 fix image_url bug
8c1afe5
@juanesarango
🐛 fix image_url prefix
47dd331
@juanesarango
🐛 try get local singularity image with retry and timeout
92a878b
@juanesarango
🐛 increase timeout
e2d5a72
@juanesarango
🐛 change to Popen to use same shell
7cc3e21
@juanesarango
🐛 use regular python glob
fc6c030
@juanesarango
🐛 fix bug with glob
01e0a28
@juanesarango
🐛 fix toil docker:// format
a4cca03
@juanesarango
🔧 use $TMP string as default and not the actual value
50d550d
@juanesarango
🔧 fix image search assertion
cb77e2c
@juanesarango
Merge branch 'master' into force
f7252fc
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@juanesarango