{"action":"created","issue":{"url":"https://api.github.com/repos/genialis/resolwe-bio/issues/610","repository_url":"https://api.github.com/repos/genialis/resolwe-bio","labels_url":"https://api.github.com/repos/genialis/resolwe-bio/issues/610/labels{/name}","comments_url":"https://api.github.com/repos/genialis/resolwe-bio/issues/610/comments","events_url":"https://api.github.com/repos/genialis/resolwe-bio/issues/610/events","html_url":"https://github.com/genialis/resolwe-bio/pull/610","id":345413574,"node_id":"MDExOlB1bGxSZXF1ZXN0MjA0NTczNDc5","number":610,"title":"[WIP] Add regtools to resolwebio/rnaseq Docker image","user":{"login":"tristanbrown","id":15306522,"node_id":"MDQ6VXNlcjE1MzA2NTIy","avatar_url":"https://avatars1.githubusercontent.com/u/15306522?v=4","gravatar_id":"","url":"https://api.github.com/users/tristanbrown","html_url":"https://github.com/tristanbrown","followers_url":"https://api.github.com/users/tristanbrown/followers","following_url":"https://api.github.com/users/tristanbrown/following{/other_user}","gists_url":"https://api.github.com/users/tristanbrown/gists{/gist_id}","starred_url":"https://api.github.com/users/tristanbrown/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tristanbrown/subscriptions","organizations_url":"https://api.github.com/users/tristanbrown/orgs","repos_url":"https://api.github.com/users/tristanbrown/repos","events_url":"https://api.github.com/users/tristanbrown/events{/privacy}","received_events_url":"https://api.github.com/users/tristanbrown/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-07-28T03:20:02Z","updated_at":"2018-07-30T13:20:23Z","closed_at":null,"author_association":"CONTRIBUTOR","pull_request":{"url":"https://api.github.com/repos/genialis/resolwe-bio/pulls/610","html_url":"https://github.com/genialis/resolwe-bio/pull/610","diff_url":"https://github.com/genialis/resolwe-bio/pull/610.diff","patch_url":"https://github.com/genialis/resolwe-bio/pull/610.patch"},"body":"## Checklist\r\n<!--\r\nMark an `[x]` for completed items.\r\n-->\r\n\r\n* [ ] Update CHANGELOG.rst for each commit separately:\r\n  * Pay attention to write entries under the \"Unreleased\" section.\r\n  * Mark all breaking changes as \"**BACKWARD INCOMPATIBLE:**\" and put them\r\n    before non-breaking changes.\r\n  * If a commit modifies a feature listed under \"Unreleased\" section,\r\n    it might be sufficient to modify the existing CHANGELOG entry from previous\r\n    commit(s).\r\n* [ ] Bump the process version:\r\n  * **MAJOR version (first number)**: Backward incompatible changes (changes\r\n    that break the api/interface). Examples: renaming the input/output, adding\r\n    mandatory input, removing input/output...\r\n  * **MINOR version (middle number)**: add functionality or changes in a\r\n    backwards-compatible manner. Examples: add output field, add non-mandatory\r\n    input parameter, use a different tool that produces same results...\r\n  * **PATCH version (last number)**: changes/bug fixes that do not affect\r\n    the api/interface. Examples: typo fix, change/add warning messages...\r\n* [ ] All inputs are used in process.\r\n* [ ] All output fields have their ``re-save`` calls.\r\n\r\n<!--\r\nRead the following guidelines and remove them before opening the pull request.\r\n-->\r\n\r\n## Additional guidelines\r\n\r\n### Processes ###\r\n\r\n* Code that was once accepted should be kept like it is. It should be changed\r\n  only when its functionality has changed. Small parts may be changed\r\n  to fix bugs (by changing code only to make it nicer you might introduce a bug).\r\n* Set the optimal number of cores that the tool can use (check if parallelization\r\n  can be performed).\r\n* Description of tool should be self explanatory with links to tool's homepage\r\n  and publication.\r\n* Write explanatory input labels and add short command line parameter names\r\n  in square brackets (for example: Maximum length [``--maxlength``]).\r\n* Where possible provide default values for the process input fields.\r\n  If they are provided, then ``required: false`` is not needed.\r\n* Add descriptive error and warning messages.\r\n* Place a ``re-checkrc`` call after each process step (call of a tool, a\r\n  Bash command, a Python script or an R script).\r\n* Add ``re-progress`` calls where appropriate.\r\n\r\n### Commit and PR messages ###\r\n\r\n* Each commit should be minimal (i.e. 1 change) and self-contained (including\r\n  tests).\r\n* Changes to Docker images need to be accepted in a separate pull request.\r\n  Before the new images can be used for automated testing of your PR, they\r\n  must be manually tagged and pushed to Docker Hub.\r\n* Mark incomplete PRs with the [WIP] (Work In Progress) tag.\r\n* Do not paste links to private repositories from the public one.\r\n\r\n### Tests ###\r\n\r\n* Add meaningful names of test files with spaces:\r\n  * Genomes: ``genome species.fa.gz``\r\n  * Annotations: ``annotation species.gtf.gz``\r\n  * Adapters: ``adapters-name/type-source``.\r\n* Output and specific input files should include the name of the tested tool.\r\n* Keep test files' size small. If there is no other option, add the large\r\n  test file to the ``files/large`` directory so it will be tracked with Git LFS.\r\n* Pay attention to edge cases: what will happen if any data is\r\n  missing, if length of some list is 0, if string is given where one expects\r\n  integer, if file is empty, ...\r\n* When testing workflows, try to verify workflow success by checking one\r\n  of the last steps. Pick the one that is most likely to fail. Also test\r\n  that all steps have 'OK' status.\r\n\r\n<!--\r\nThanks!\r\n-->\r\n"},"comment":{"url":"https://api.github.com/repos/genialis/resolwe-bio/issues/comments/408860470","html_url":"https://github.com/genialis/resolwe-bio/pull/610#issuecomment-408860470","issue_url":"https://api.github.com/repos/genialis/resolwe-bio/issues/610","id":408860470,"node_id":"MDEyOklzc3VlQ29tbWVudDQwODg2MDQ3MA==","user":{"login":"mstajdohar","id":1026716,"node_id":"MDQ6VXNlcjEwMjY3MTY=","avatar_url":"https://avatars1.githubusercontent.com/u/1026716?v=4","gravatar_id":"","url":"https://api.github.com/users/mstajdohar","html_url":"https://github.com/mstajdohar","followers_url":"https://api.github.com/users/mstajdohar/followers","following_url":"https://api.github.com/users/mstajdohar/following{/other_user}","gists_url":"https://api.github.com/users/mstajdohar/gists{/gist_id}","starred_url":"https://api.github.com/users/mstajdohar/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mstajdohar/subscriptions","organizations_url":"https://api.github.com/users/mstajdohar/orgs","repos_url":"https://api.github.com/users/mstajdohar/repos","events_url":"https://api.github.com/users/mstajdohar/events{/privacy}","received_events_url":"https://api.github.com/users/mstajdohar/received_events","type":"User","site_admin":false},"created_at":"2018-07-30T13:20:23Z","updated_at":"2018-07-30T13:20:23Z","author_association":"MEMBER","body":"The image fails to build locally (`docker build -t rnaseq .`). It seams that `cmake` and `make` are executed in an empty directory:\r\n\r\n```Downloading 'griffithlab/regtools' version '0.5.0'...\r\nFetching 'https://github.com/griffithlab/regtools/archive/0.5.0.tar.gz'...\r\nVerifying package...\r\nUnpacking...\r\nUsage\r\n\r\n  cmake [options] <path-to-source>\r\n  cmake [options] <path-to-existing-build>\r\n\r\nSpecify a source directory to (re-)generate a build system for it in the\r\ncurrent working directory.  Specify an existing build directory to\r\nre-generate its build system.\r\n\r\nRun 'cmake --help' for more information.\r\n\r\nmake: *** No targets specified and no makefile found.  Stop.\r\nxargs: bash: exited with status 255; aborting\r\nThe command '/bin/sh -c export DEBIAN_FRONTEND=noninteractive &&     apt-get update &&     if [ -f /var/cache/build/packages-debian.txt ]; then         echo \"Installing distribution packages (runtime requirements)...\" &&         sed -e 's/^#.*$//g' -e '/^$/d' /var/cache/build/packages-debian.txt |             xargs apt-get --no-install-recommends -y install         ;     fi &&     if [ -f /var/cache/build/packages-debian-buildreq.txt ]; then         echo \"Installing distribution packages (build requirements)...\" &&         sed -e 's/^#.*$//g' -e '/^$/d' /var/cache/build/packages-debian-buildreq.txt |             xargs apt-get --no-install-recommends -y install         ;     fi &&     if [ -f /var/cache/build/packages-python2.txt ]; then         echo \"Installing Python 2 packages...\" &&         pip install --require-hashes --requirement /var/cache/build/packages-python2.txt         ;     fi &&     if [ -f /var/cache/build/packages-python2-stage2.txt ]; then         echo \"Installing stage 2 Python 2 packages...\" &&         pip install --require-hashes --requirement /var/cache/build/packages-python2-stage2.txt         ;     fi &&     if [ -f /var/cache/build/packages-python3.txt ]; then         echo \"Installing Python 3 packages...\" &&         pip3 install --require-hashes --requirement /var/cache/build/packages-python3.txt         ;     fi &&     if [ -f /var/cache/build/packages-python3-stage2.txt ]; then         echo \"Installing stage 2 Python 3 packages...\" &&         pip3 install --require-hashes --requirement /var/cache/build/packages-python3-stage2.txt         ;     fi &&     if [ -f /var/cache/build/packages-manual.txt ]; then         echo \"Building manual packages...\" &&         sed -e 's/^#.*$//g' -e '/^$/d' /var/cache/build/packages-manual.txt |             xargs --max-args 1 -I '{}' bash -c 'bash /var/cache/build/packages-manual/{}.sh || exit 255'         ;     fi &&     echo \"Cleaning up packages...\" &&     if [ -f /var/cache/build/packages-debian-buildreq.txt ]; then         sed -e 's/^#.*$//g' -e '/^$/d' /var/cache/build/packages-debian-buildreq.txt |             xargs apt-get -y purge         ;     fi &&     apt-get autoremove --purge -y &&     apt-get clean &&     rm -rf /var/lib/apt/lists/* &&     rm -rf /root/.cache/pip &&     rm -rf /tmp/*' returned a non-zero code: 124```"}}
{"actor":{"display_login":"mstajdohar"}}