{"action":"created","issue":{"url":"https://api.github.com/repos/ttimbers/studyGroup/issues/6","labels_url":"https://api.github.com/repos/ttimbers/studyGroup/issues/6/labels{/name}","comments_url":"https://api.github.com/repos/ttimbers/studyGroup/issues/6/comments","events_url":"https://api.github.com/repos/ttimbers/studyGroup/issues/6/events","html_url":"https://github.com/ttimbers/studyGroup/issues/6","id":90191852,"number":6,"title":"Using Make to increase Automation & Reproducibility by Shaun Jackman","user":{"login":"ttimbers","id":6865016,"avatar_url":"https://avatars.githubusercontent.com/u/6865016?v=3","gravatar_id":"","url":"https://api.github.com/users/ttimbers","html_url":"https://github.com/ttimbers","followers_url":"https://api.github.com/users/ttimbers/followers","following_url":"https://api.github.com/users/ttimbers/following{/other_user}","gists_url":"https://api.github.com/users/ttimbers/gists{/gist_id}","starred_url":"https://api.github.com/users/ttimbers/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ttimbers/subscriptions","organizations_url":"https://api.github.com/users/ttimbers/orgs","repos_url":"https://api.github.com/users/ttimbers/repos","events_url":"https://api.github.com/users/ttimbers/events{/privacy}","received_events_url":"https://api.github.com/users/ttimbers/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/ttimbers/studyGroup/labels/workshop","name":"workshop","color":"009800"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":14,"created_at":"2015-06-22T19:41:48Z","updated_at":"2015-08-13T21:28:29Z","closed_at":null,"body":"# Details\r\n\r\n**Where**: Simon Fraser University, Burnaby Campus, SSB 7172\r\n**When**: 3:30 pm - 4:30 pm, Tuesday, August 11, 2015\r\n**Livevstream:** [Google Hangouts On Air](https://plus.google.com/events/csvbopu1h8lk35r741hf5veh97s)\r\n**Public notepad** for this session can be accessed [here](https://etherpad.mozilla.org/2015-08-11-SFU).\r\n**Lesson notes** can be found [here](https://stat545-ubc.github.io/automation00_index.html).\r\n\r\n**Dependencies**: Bash Shell and Make\r\n\r\n# Setup\r\n\r\n## Windows\r\n\r\n### Bash\r\n\r\nInstall Git for Windows by downloading and running the installer (http://msysgit.github.io/). This will    provide you with both Git and Bash in the Git Bash program.\r\n\r\n### Make\r\n\r\n1. Download make.exe from here: https://github.com/msysgit/msysgit/blob/master/bin/make.exe?raw=true \r\n\r\n2. Place it in the bin directory where you installed Git Bash e.g. C:\\Program Files (x86)\\Git\\bin \r\n\r\n3. To test: open a Git Bash window, type make, and press Enter \r\n\r\n4. You should see the following message \r\n\r\n  ```\r\n  make: *** No targets specified and no makefile found. Stop.\r\n  ```\r\n\r\n  This means that Make was successfully installed. Otherwise, you'll see this error message:\r\n\r\n  ```\r\n  bash: make: command not found\r\n  ```\r\n\r\n## Mac OS X\r\n\r\n### Bash\r\n\r\nThe default shell in all versions of Mac OS X is bash, so no need to install anything. You access bash from the Terminal (found in `/Applications/Utilities`). You may want to keep Terminal in your dock for this workshop.\r\n\r\n### Make\r\n\r\nMake doesn't come by default with OS X. You need to install a package called Command Line Tools. If you're running one of the latest versions of OS X (10.9 or later), you can easily do so by running the following command. \r\n\r\n*You can find out which version of OS X you're running by clicking the Apple icon () at the top-left of your screen and selecting \"About This Mac\".*\r\n\r\n```\r\nxcode-select  --install\r\n```\r\n\r\nHowever, if you're running an older version of OS X (10.8 or earlier), you have a bit more work to do : \r\n\r\n1. Visit the [Downloads section of the Apple Developer website](https://developer.apple.com/downloads/) and login using your Apple ID. If you don't have one, you can create a dummy one without giving personal information. \r\n\r\n2. Search for \"command line tools\" using the search box on the left. \r\n\r\n3. Find the Command Line Tools for your version of OS X.  **Avoid versions labelled as beta; these might not work as expected.**\r\n\r\n4. Double-click that Command Line Tools (or click the plus sign on the left) and download the file using the link on the right. \r\n\r\n5. Install the Command Line Tools by mounting the downloaded DMG file and launching the installer. \r\n\r\n## Linux\r\n\r\nBash and make are typically included with any Linux distribution. Also, bash is usually the default shell. If not, you can just open a Terminal window and run the command `bash`. "},"comment":{"url":"https://api.github.com/repos/ttimbers/studyGroup/issues/comments/130849565","html_url":"https://github.com/ttimbers/studyGroup/issues/6#issuecomment-130849565","issue_url":"https://api.github.com/repos/ttimbers/studyGroup/issues/6","id":130849565,"user":{"login":"pditommaso","id":816968,"avatar_url":"https://avatars.githubusercontent.com/u/816968?v=3","gravatar_id":"","url":"https://api.github.com/users/pditommaso","html_url":"https://github.com/pditommaso","followers_url":"https://api.github.com/users/pditommaso/followers","following_url":"https://api.github.com/users/pditommaso/following{/other_user}","gists_url":"https://api.github.com/users/pditommaso/gists{/gist_id}","starred_url":"https://api.github.com/users/pditommaso/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pditommaso/subscriptions","organizations_url":"https://api.github.com/users/pditommaso/orgs","repos_url":"https://api.github.com/users/pditommaso/repos","events_url":"https://api.github.com/users/pditommaso/events{/privacy}","received_events_url":"https://api.github.com/users/pditommaso/received_events","type":"User","site_admin":false},"created_at":"2015-08-13T21:28:28Z","updated_at":"2015-08-13T21:28:28Z","body":"@radaniba That's really a great idea. Count on my help regarding Nextflow.\r\n\r\n@sjackman Thanks to mention the list. About `make`, I didn't include it because the list started as a collection of niche projects and tools specifically designed for workflow and pipeline management, instead `make` strictly speaking is a build automation tool.  "}}