{"action":"created","issue":{"url":"https://api.github.com/repos/marbl/metAMOS/issues/180","labels_url":"https://api.github.com/repos/marbl/metAMOS/issues/180/labels{/name}","comments_url":"https://api.github.com/repos/marbl/metAMOS/issues/180/comments","events_url":"https://api.github.com/repos/marbl/metAMOS/issues/180/events","html_url":"https://github.com/marbl/metAMOS/issues/180","id":57763427,"number":180,"title":"Test suite errors.","user":{"login":"JustGitting","id":6530017,"avatar_url":"https://avatars.githubusercontent.com/u/6530017?v=3","gravatar_id":"","url":"https://api.github.com/users/JustGitting","html_url":"https://github.com/JustGitting","followers_url":"https://api.github.com/users/JustGitting/followers","following_url":"https://api.github.com/users/JustGitting/following{/other_user}","gists_url":"https://api.github.com/users/JustGitting/gists{/gist_id}","starred_url":"https://api.github.com/users/JustGitting/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/JustGitting/subscriptions","organizations_url":"https://api.github.com/users/JustGitting/orgs","repos_url":"https://api.github.com/users/JustGitting/repos","events_url":"https://api.github.com/users/JustGitting/events{/privacy}","received_events_url":"https://api.github.com/users/JustGitting/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-02-16T04:11:00Z","updated_at":"2015-02-17T22:48:37Z","closed_at":null,"body":"Hi everyone,\r\n\r\nI've been trying to run the test suite after installing metAMOS from the git clone of 1.5rc3.\r\n\r\n```\r\n$ git clone --branch \"v1.5rc3\" https://github.com/marbl/metAMOS.git\r\n$ mv metAMOS/ metAMOS-1.5rc3_git\r\n```\r\n\r\nI had to run the INSTALL script a few times before it completed successfully.\r\n\r\n```\r\n$ export http_proxy=\"http://proxy.abc.com:8080\"\r\n$ export ftp_proxy=\"ftp://proxy.abc.com:8080\"\r\n$ python INSTALL.py core imetamos optional\r\n```\r\n\r\nI've run the check installation script with the following results.\r\n\r\n```\r\n$ python  ./check_install.py ./ allfiles.txt\r\nInstallation in ./ looks ok, have fun!\r\n```\r\n\r\nHowever, using the \"required files list\" fails, and the \".//Utilities/cpp/Linux-x86_64/MetaVelvet/scripts\" does not even exist.\r\n\r\n```\r\n$ python  ./check_install.py ./ required_file_list.txt\r\nERROR: Required file .//Utilities/cpp/Linux-x86_64/MetaVelvet/scripts/shuffleSequences_fasta.pl not found! Please reinstall MetAMOS\r\n```\r\n\r\nI've tried reinstalling MetAMOS, but it does not have any errors:\r\n\r\n```\r\n$ python INSTALL.py core imetamos optional\r\n<<Welcome to metAMOS install>>\r\nSelected to install workflowName: CORE.\r\nSelected to install workflowName: OPTIONAL.\r\nSelected to install workflowName: IMETAMOS.\r\nWill automatically install:\r\n        Pysam\r\n        Fastqc\r\n        Ca\r\n        Ale\r\n        Sga\r\n        Velvet-Sc\r\n        Metaphyler\r\n        Phylosift\r\n        Metavelvet\r\n        Velvet\r\n        Soap2\r\n        Frcbam\r\n        Quast\r\n        Eautils\r\n        Ray\r\n        Numpy\r\n        Freebayes\r\n        Fcp\r\n        Edena\r\n        Uniprot\r\n        Cython\r\n        Cgal\r\n        Mira\r\n        Matplotlib\r\n        Prokka\r\n        Idba\r\n        Cmake\r\n        Lap\r\n        Masurca\r\n        Kronatools\r\n        Abyss\r\n        Sra\r\n        Spades\r\n        Kraken\r\n        Psutil\r\n        Setuptools\r\n        Amos\r\n        Phmmer\r\n        Kmergenie\r\n        Reapr\r\nFound jellyfish v2.1.3\r\nKraken requires jellyfish version 1\r\nChecking whether refseq_protein is complete. Expecting 17 partitions.\r\n\r\nRun setup.py..\r\nrunning install_scripts\r\nrunning egg_info\r\nwriting metAMOS.egg-info/PKG-INFO\r\nwriting top-level names to metAMOS.egg-info/top_level.txt\r\nwriting dependency_links to metAMOS.egg-info/dependency_links.txt\r\nreading manifest file 'metAMOS.egg-info/SOURCES.txt'\r\nwriting manifest file 'metAMOS.egg-info/SOURCES.txt'\r\nrunning build_scripts\r\ncopying build/scripts-2.7/runPipeline.py -> /group/metagen/dbtools/src/metAMOS-1.5rc3_git\r\ncopying build/scripts-2.7/initPipeline.py -> /group/metagen/dbtools/src/metAMOS-1.5rc3_git\r\nchanging mode of /group/metagen/dbtools/src/metAMOS-1.5rc3_git/runPipeline.py to 755\r\nchanging mode of /group/metagen/dbtools/src/metAMOS-1.5rc3_git/initPipeline.py to 755\r\nrunning build_ext\r\nskipping './src/preprocess.c' Cython extension (up-to-date)\r\nskipping './src/annotate.c' Cython extension (up-to-date)\r\nskipping './src/fannotate.c' Cython extension (up-to-date)\r\nskipping './src/mapreads.c' Cython extension (up-to-date)\r\nskipping './src/findorfs.c' Cython extension (up-to-date)\r\nskipping './src/findscforfs.c' Cython extension (up-to-date)\r\nskipping './src/scaffold.c' Cython extension (up-to-date)\r\n```\r\n\r\n\r\nPushing ahead, I still try to run the test scripts, which fail because they are unable to find the test data sets, which do exist in the Test/ directory.\r\n\r\n```\r\n$ cd Test/\r\n$ ./run_pipeline_test.sh\r\nWarning: Celera Assembler is not found, some functionality will not be available\r\nWarning: BLASR is not found, some functionality will not be available\r\nWarning: SignalP+ is not found, some functionality will not be available\r\nWarning: FRCbam is not found, some functionality will not be available\r\nError, provided files do not exist:\r\nFile carsonella_pe_filt.fna from library 1 does not exist\r\n\r\nproject dir /group/metagen/dbtools/src/metAMOS-1.5rc3_git/Test/test1 does not exist!\r\n<< SNIP >>\r\n```\r\n```\r\n$ ls *.fna\r\nMA_test2.filt2.fna  carsonella_pe_filt.fna  carsonella_reference.fna\r\n```\r\n\r\nIt would appear the initPipeLine script is unable to find the fna files in the Test directory. Have I missed setting a PATH?\r\n\r\nCheers\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/marbl/metAMOS/issues/comments/74772133","html_url":"https://github.com/marbl/metAMOS/issues/180#issuecomment-74772133","issue_url":"https://api.github.com/repos/marbl/metAMOS/issues/180","id":74772133,"user":{"login":"skoren","id":923478,"avatar_url":"https://avatars.githubusercontent.com/u/923478?v=3","gravatar_id":"","url":"https://api.github.com/users/skoren","html_url":"https://github.com/skoren","followers_url":"https://api.github.com/users/skoren/followers","following_url":"https://api.github.com/users/skoren/following{/other_user}","gists_url":"https://api.github.com/users/skoren/gists{/gist_id}","starred_url":"https://api.github.com/users/skoren/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/skoren/subscriptions","organizations_url":"https://api.github.com/users/skoren/orgs","repos_url":"https://api.github.com/users/skoren/repos","events_url":"https://api.github.com/users/skoren/events{/privacy}","received_events_url":"https://api.github.com/users/skoren/received_events","type":"User","site_admin":false},"created_at":"2015-02-17T22:48:37Z","updated_at":"2015-02-17T22:48:37Z","body":"That is very strange because initPipeline just checks if the file is remote and if not checks os.path.exists. Can you modify initPipeline to add some debug output:\r\nline 125-126\r\n```\r\ndef isSRAID(file):\r\n   return utils.translateToSRAURL(settings, file) != \"\"\r\n```\r\n\r\nchange to\r\n\r\n```\r\ndef isSRAID(file):\r\n   print \"The path returns %s aka %s\"%(utils.translateToSRAURL(settings, file), (utils.translateToSRAURL(settings, file) != \"\"))\r\n   return utils.translateToSRAURL(settings, file) != \"\"\r\n```\r\n\r\nand line 129-130:\r\n\r\n```\r\ndef isRemote(file):\r\n   return isSRAID(file) or file.startswith(\"ftp://\") or file.startswith(\"http://\") or file.startswith(\"https://\")\r\n```\r\nchange to\r\n\r\n```\r\ndef isRemote(file):\r\n    print \"The file %s is SRA: %s FTP: %s http %s https %s\\n\"%(file, isSRAID(file), file.startswith(\"ftp://\"), file.s    tartswith(\"http://\"),  file.startswith(\"https://\"))\r\n    return isSRAID(file) or file.startswith(\"ftp://\") or file.startswith(\"http://\") or file.startswith(\"https://\")\r\n```"}}