{"action":"created","issue":{"url":"https://api.github.com/repos/statgen/gotcloud/issues/14","labels_url":"https://api.github.com/repos/statgen/gotcloud/issues/14/labels{/name}","comments_url":"https://api.github.com/repos/statgen/gotcloud/issues/14/comments","events_url":"https://api.github.com/repos/statgen/gotcloud/issues/14/events","html_url":"https://github.com/statgen/gotcloud/issues/14","id":120304126,"number":14,"title":"Align test fails using gotcloud.1.17.5","user":{"login":"mkolovic","id":15839101,"avatar_url":"https://avatars.githubusercontent.com/u/15839101?v=3","gravatar_id":"","url":"https://api.github.com/users/mkolovic","html_url":"https://github.com/mkolovic","followers_url":"https://api.github.com/users/mkolovic/followers","following_url":"https://api.github.com/users/mkolovic/following{/other_user}","gists_url":"https://api.github.com/users/mkolovic/gists{/gist_id}","starred_url":"https://api.github.com/users/mkolovic/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mkolovic/subscriptions","organizations_url":"https://api.github.com/users/mkolovic/orgs","repos_url":"https://api.github.com/users/mkolovic/repos","events_url":"https://api.github.com/users/mkolovic/events{/privacy}","received_events_url":"https://api.github.com/users/mkolovic/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-12-04T00:26:19Z","updated_at":"2015-12-10T00:31:27Z","closed_at":null,"body":"I am configuring a Docker image to run GotCloud. Below are the steps taken while testing on a base image with all the requirements. \r\n\r\n```\r\n$ wget https://github.com/statgen/gotcloud/archive/gotcloud.1.17.5.tar.gz\r\n$ tar -xzf gotcloud.1.17.5.tar.gz -C /usr/local\r\n$ cd /usr/local/gotcloud-gotcloud.1.17.5/src\r\n$ make\r\n$ cd /usr/local/gotcloud-gotcloud.1.17.5\r\n$ scripts/check_requirements.sh\r\nWARNING:  '/usr/local/gotcloud/bin' does not exist.  Continuing...\r\nGood, you appear to have 'java' installed\r\nGood, you appear to have 'make' installed\r\nGood, you appear to have 'libssl' installed at the correct level\r\n#============================================================\r\n#   '/usr/local/gotcloud/test/umake' does not exist so you cannot test this install\r\n#   Install it by doing 'sudo dpkg -i gotcloud-test_*.deb'\r\n#============================================================\r\n```\r\nSo it is not recognizing that gotcloud exists due to the specific version name, I realize that if I did a `git clone` this issue would not arise, or I could move `gotcloud-gotcloud.1.17.5` to `gotcloud`. Proceeding...\r\n\r\n```\r\n$ ./gotcloud align --test /root/testalign\r\nRemoving any previous results from: /root/testalign/aligntest\r\nRunning GOTCLOUD TEST, test log in: /root/testalign/aligntest.log\r\nFile sizes of 10 FASTQ input files referenced in '/usr/local/gotcloud-gotcloud.1.17.5/test/align/indexFile.txt' = 0.00 GB\r\nTotal temp space will be about 0.00 GB\r\nTotal space for BAM files will be about 0.00 GB\r\nBe sure you have enough space to hold all this data\r\nCreated /root/testalign/aligntest/Makefiles/align_Sample1.Makefile\r\nCreated /root/testalign/aligntest/Makefiles/align_Sample2.Makefile\r\nCreated /root/testalign/aligntest/Makefiles/align_Sample3.Makefile\r\n---------------------------------------------------------------------\r\nWaiting while samples are processed...\r\nRunning make -f /root/testalign/aligntest/Makefiles/alignAll.Makefile > /root/testalign/aligntest/Makefiles/alignAll.Makefile.log 2> /root/testalign/aligntest/Makefiles/alignAll.Makefile.err...\r\n\r\nProcessing finished in 68 secs with no errors reported\r\nUse of uninitialized value $ENV{\"USER\"} in concatenation (.) or string at /usr/local/gotcloud-gotcloud.1.17.5/scripts/runcluster.pl line 36.\r\nUse of uninitialized value $ENV{\"USER\"} in concatenation (.) or string at /usr/local/gotcloud-gotcloud.1.17.5/scripts/runcluster.pl line 36.\r\nUse of uninitialized value $ENV{\"USER\"} in concatenation (.) or string at /usr/local/gotcloud-gotcloud.1.17.5/scripts/runcluster.pl line 36.\r\nUse of uninitialized value $ENV{\"USER\"} in concatenation (.) or string at /usr/local/gotcloud-gotcloud.1.17.5/scripts/runcluster.pl line 36.\r\nResults from DIFF will be in /root/testalign/diff_logfiles_results.txt\r\nFailed Makefile results validation. See mismatches in /root/testalign/diff_logfiles_results.txt\r\nComparison failed, test case FAILED.\r\nCMD=/usr/local/gotcloud-gotcloud.1.17.5/scripts/diff_results_align.sh /root/testalign /usr/local/gotcloud-gotcloud.1.17.5/test/align/expected\r\n```\r\n\r\nSo it seems as though the fastq files are not being recognized since it claims a total size of 0GB for them, even though the path to the files is correct. Please let me know if additional information is required, thanks."},"comment":{"url":"https://api.github.com/repos/statgen/gotcloud/issues/comments/163447210","html_url":"https://github.com/statgen/gotcloud/issues/14#issuecomment-163447210","issue_url":"https://api.github.com/repos/statgen/gotcloud/issues/14","id":163447210,"user":{"login":"pjvandehaar","id":862089,"avatar_url":"https://avatars.githubusercontent.com/u/862089?v=3","gravatar_id":"","url":"https://api.github.com/users/pjvandehaar","html_url":"https://github.com/pjvandehaar","followers_url":"https://api.github.com/users/pjvandehaar/followers","following_url":"https://api.github.com/users/pjvandehaar/following{/other_user}","gists_url":"https://api.github.com/users/pjvandehaar/gists{/gist_id}","starred_url":"https://api.github.com/users/pjvandehaar/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pjvandehaar/subscriptions","organizations_url":"https://api.github.com/users/pjvandehaar/orgs","repos_url":"https://api.github.com/users/pjvandehaar/repos","events_url":"https://api.github.com/users/pjvandehaar/events{/privacy}","received_events_url":"https://api.github.com/users/pjvandehaar/received_events","type":"User","site_admin":false},"created_at":"2015-12-10T00:31:27Z","updated_at":"2015-12-10T00:31:27Z","body":"That particular commit only affects the tests.  Since the last release we've fixed a few bugs, but I can just make a new release when your Dockerfile is ready.\r\n\r\nYes, those results for `gotcloud test` indicate success.  I've just made another change to make that more obvious.\r\n\r\nIf you want to use `gotcloud genomestrip`, you'll need to change a couple things."}}