{"action":"created","issue":{"url":"https://api.github.com/repos/nextflow-io/nextflow/issues/698","repository_url":"https://api.github.com/repos/nextflow-io/nextflow","labels_url":"https://api.github.com/repos/nextflow-io/nextflow/issues/698/labels{/name}","comments_url":"https://api.github.com/repos/nextflow-io/nextflow/issues/698/comments","events_url":"https://api.github.com/repos/nextflow-io/nextflow/issues/698/events","html_url":"https://github.com/nextflow-io/nextflow/issues/698","id":323014258,"node_id":"MDU6SXNzdWUzMjMwMTQyNTg=","number":698,"title":"K8s permission problems for scripts in `bin` folder","user":{"login":"wikiselev","id":2342606,"node_id":"MDQ6VXNlcjIzNDI2MDY=","avatar_url":"https://avatars2.githubusercontent.com/u/2342606?v=4","gravatar_id":"","url":"https://api.github.com/users/wikiselev","html_url":"https://github.com/wikiselev","followers_url":"https://api.github.com/users/wikiselev/followers","following_url":"https://api.github.com/users/wikiselev/following{/other_user}","gists_url":"https://api.github.com/users/wikiselev/gists{/gist_id}","starred_url":"https://api.github.com/users/wikiselev/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wikiselev/subscriptions","organizations_url":"https://api.github.com/users/wikiselev/orgs","repos_url":"https://api.github.com/users/wikiselev/repos","events_url":"https://api.github.com/users/wikiselev/events{/privacy}","received_events_url":"https://api.github.com/users/wikiselev/received_events","type":"User","site_admin":false},"labels":[{"id":922936077,"node_id":"MDU6TGFiZWw5MjI5MzYwNzc=","url":"https://api.github.com/repos/nextflow-io/nextflow/labels/platform/k8s","name":"platform/k8s","color":"4025a3","default":false},{"id":921273768,"node_id":"MDU6TGFiZWw5MjEyNzM3Njg=","url":"https://api.github.com/repos/nextflow-io/nextflow/labels/triage/needs-information","name":"triage/needs-information","color":"958ad8","default":false}],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":13,"created_at":"2018-05-14T23:18:22Z","updated_at":"2018-06-11T14:40:54Z","closed_at":"2018-05-29T15:18:04Z","author_association":"CONTRIBUTOR","body":"Hi Paolo,\r\n\r\nFor the same pipeline that work no problem on LSF I get a permission error when running on K8s:\r\n```\r\n[warm up] executor > k8s\r\n[f7/cf7557] Submitted process > irods (ImmHet6564351)\r\n[c3/bac014] Submitted process > irods (ImmHet6564353)\r\n[41/cbf3d4] Submitted process > irods (ImmHet6564350)\r\n[d8/815486] Submitted process > irods (ImmHet6564354)\r\n[09/a15092] Submitted process > irods (ImmHet6564352)\r\nERROR ~ Error executing process > 'irods (ImmHet6564351)'\r\n\r\nCaused by:\r\n  Process `irods (ImmHet6564351)` terminated with an error exit status (126)\r\n\r\nCommand executed:\r\n\r\n  irods.sh ImmHet6564351\r\n\r\nCommand exit status:\r\n  126\r\n\r\nCommand output:\r\n  (empty)\r\n\r\nCommand error:\r\n  .command.stub: line 38: ps: command not found\r\n  .command.sh: line 2: /mnt/gluster/projects/cellgeni/rnaseq-noqc/bin/irods.sh: Permission denied\r\n  .command.stub: line 27: ps: command not found\r\n  .command.stub: line 12: ps: command not found\r\n  .command.stub: line 99:    32 Terminated              nxf_trace \"$pid\" .command.trace\r\n```\r\nWhen I look in the local version of the pipeline the file permissions are not executable:\r\n```\r\nubuntu@vlad-k8s-test-k8s-master-nf-1:/mnt/gluster/pvc-319c8c17-3ca6-11e8-89b1-fa163e31bb09$ ls -la projects/cellgeni/rnaseq-noqc/bin/\r\ntotal 24\r\ndrwxr-xr-x  2 root root 4096 May 14 23:13 .\r\ndrwxr-xr-x 10 root root 4096 May 14 23:13 ..\r\n-rw-r--r--  1 root root 3647 May 14 23:13 dupRadar.r\r\n-rw-r--r--  1 root root 2271 May 14 23:13 edgeR_heatmap_MDS.r\r\n-rw-r--r--  1 root root 3763 May 14 23:13 gtf2bed\r\n-rw-r--r--  1 root root  305 May 14 23:13 irods.sh\r\n-rw-r--r--  1 root root  994 May 14 23:13 markdown_to_html.r\r\n-rw-r--r--  1 root root 2912 May 14 23:13 merge_featurecounts.py\r\n-rw-r--r--  1 root root  542 May 14 23:13 merge_salmon.R\r\n```\r\nIn a local version of the same pipeline on the LSF farm all these files are executable:\r\n```\r\nvk6@bc-26-3-14:/lustre/scratch117/cellgen/cellgeni/tic-24test$ ls -la ~/.nextflow/assets/cellgeni/rnaseq-noqc/bin/\r\ntotal 36\r\ndrwxr-sr-x  2 vk6 team218 4096 May 14 21:25 .\r\ndrwxr-sr-x 10 vk6 team218 4096 May 14 17:18 ..\r\n-rwxr-xr-x  1 vk6 team218 3647 Apr 23 17:38 dupRadar.r\r\n-rwxr-xr-x  1 vk6 team218 2271 Apr 23 17:38 edgeR_heatmap_MDS.r\r\n-rwxr-xr-x  1 vk6 team218 3763 Apr 23 17:38 gtf2bed\r\n-rwxr-xr-x  1 vk6 team218  305 May 14 21:25 irods.sh\r\n-rwxr-xr-x  1 vk6 team218  994 Apr 23 17:38 markdown_to_html.r\r\n-rwxr-xr-x  1 vk6 team218 2912 Apr 23 17:38 merge_featurecounts.py\r\n-rwxr-xr-x  1 vk6 team218  542 Apr 24 22:54 merge_salmon.R\r\n```"},"comment":{"url":"https://api.github.com/repos/nextflow-io/nextflow/issues/comments/396267629","html_url":"https://github.com/nextflow-io/nextflow/issues/698#issuecomment-396267629","issue_url":"https://api.github.com/repos/nextflow-io/nextflow/issues/698","id":396267629,"node_id":"MDEyOklzc3VlQ29tbWVudDM5NjI2NzYyOQ==","user":{"login":"wikiselev","id":2342606,"node_id":"MDQ6VXNlcjIzNDI2MDY=","avatar_url":"https://avatars2.githubusercontent.com/u/2342606?v=4","gravatar_id":"","url":"https://api.github.com/users/wikiselev","html_url":"https://github.com/wikiselev","followers_url":"https://api.github.com/users/wikiselev/followers","following_url":"https://api.github.com/users/wikiselev/following{/other_user}","gists_url":"https://api.github.com/users/wikiselev/gists{/gist_id}","starred_url":"https://api.github.com/users/wikiselev/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wikiselev/subscriptions","organizations_url":"https://api.github.com/users/wikiselev/orgs","repos_url":"https://api.github.com/users/wikiselev/repos","events_url":"https://api.github.com/users/wikiselev/events{/privacy}","received_events_url":"https://api.github.com/users/wikiselev/received_events","type":"User","site_admin":false},"created_at":"2018-06-11T14:40:53Z","updated_at":"2018-06-11T14:40:53Z","author_association":"CONTRIBUTOR","body":"Hi @pditommaso , I can now confirm that adding `bash` to the scripts worked! Thanks, Vlad"}}
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