{"_id":"59e4b76a334cf10026e3b164","project":"55faf11ba62ba1170021a9a7","version":{"_id":"55faf11ba62ba1170021a9aa","project":"55faf11ba62ba1170021a9a7","__v":40,"createdAt":"2015-09-17T16:58:03.490Z","releaseDate":"2015-09-17T16:58:03.490Z","categories":["55faf11ca62ba1170021a9ab","55faf8f4d0e22017005b8272","55faf91aa62ba1170021a9b5","55faf929a8a7770d00c2c0bd","55faf932a8a7770d00c2c0bf","55faf94b17b9d00d00969f47","55faf958d0e22017005b8274","55faf95fa8a7770d00c2c0c0","55faf96917b9d00d00969f48","55faf970a8a7770d00c2c0c1","55faf98c825d5f19001fa3a6","55faf99aa62ba1170021a9b8","55faf99fa62ba1170021a9b9","55faf9aa17b9d00d00969f49","55faf9b6a8a7770d00c2c0c3","55faf9bda62ba1170021a9ba","5604570090ee490d00440551","5637e8b2fbe1c50d008cb078","5649bb624fa1460d00780add","5671974d1b6b730d008b4823","5671979d60c8e70d006c9760","568e8eef70ca1f0d0035808e","56d0a2081ecc471500f1795e","56d4a0adde40c70b00823ea3","56d96b03dd90610b00270849","56fbb83d8f21c817002af880","573c811bee2b3b2200422be1","576bc92afb62dd20001cda85","5771811e27a5c20e00030dcd","5785191af3a10c0e009b75b0","57bdf84d5d48411900cd8dc0","57ff5c5dc135231700aed806","5804caf792398f0f00e77521","58458b4fba4f1c0f009692bb","586d3c287c6b5b2300c05055","58ef66d88646742f009a0216","58f5d52d7891630f00fe4e77","59a555bccdbd85001bfb1442","5a2a81f688574d001e9934f5","5b080c8d7833b20003ddbb6f"],"is_deprecated":false,"is_hidden":false,"is_beta":true,"is_stable":true,"codename":"","version_clean":"1.0.0","version":"1.0"},"category":{"_id":"59a555bccdbd85001bfb1442","project":"55faf11ba62ba1170021a9a7","version":"55faf11ba62ba1170021a9aa","__v":0,"sync":{"url":"","isSync":false},"reference":false,"createdAt":"2017-08-29T11:53:32.348Z","from_sync":false,"order":35,"slug":"sbfs-beta","title":"SBFS (Beta)"},"user":"566590c83889610d0008a253","githubsync":"","__v":0,"parentDoc":null,"updates":[],"next":{"pages":[],"description":""},"createdAt":"2017-10-16T13:43:06.150Z","link_external":false,"link_url":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":1,"body":"##Overview\n\nInstall SBFS manually for Linux and macOS. Note that these instructions are meant for advanced users.\n\nConversely, learn to [install SBFS automatically](doc:install-sbfs-automatically).\n\n###Linux\n\n1. Download the [SBFS executable file](https://static.sbgenomics.com/sbfs/linux-amd64/sbfs).\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"curl https://igor.sbgenomics.com/downloads/sbfs/linux-amd64/sbfs -O\",\n      \"language\": \"text\",\n      \"name\": \"Downloading the SBFS\"\n    }\n  ]\n}\n[/block]\n2. Change the file permissions so you are able to run the executable\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"chmod a+x sbfs\",\n      \"language\": \"text\",\n      \"name\": \"Changing the permissions\"\n    }\n  ]\n}\n[/block]\nThe SBFS is now fully installed. See below for optional SBFS operations. \n\n###Optional operations\n\n####Add SBFS to the PATH\n\nAdd SBFS to the PATH to facilitate performing all SBFS operations using one of the following methods. Note that this is an optional step as the SBFS is also available if you provide the full path to the executable (e.g. `path/to/dir/sbfs`).\n\n* **Move SBFS binary** to a directory which is already in the PATH.\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"sudo mv sbfs /usr/local/bin/\",\n      \"language\": \"text\",\n      \"name\": \"Moving the SBFS binary\"\n    }\n  ]\n}\n[/block]\n* **Add the directory** which contains SBFS to the PATH. You can also create either a hard link or a symbolic link to the SBFS binary. \n\n\n####Add bash completion for SBFS\n\nPlease note that this only works with bash completion version 4, which should be previously installed and enabled.\n\nTo add bash completion on Linux, issue the following command:\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"sudo bash -c \\\"sbfs gen completion > /etc/bash_completion.d/sbfs\\\"\",\n      \"language\": \"text\",\n      \"name\": \"Adding bash completion on Linux\"\n    }\n  ]\n}\n[/block]\nTo complete enabling SBFS bash completion restart the terminal application or source SBFS bash completion while staying in the same terminal application with this command:\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"sudo sbfs gen man /usr/local/share/man/man1/\",\n      \"language\": \"text\",\n      \"name\": \"Enable the bash completion\"\n    }\n  ]\n}\n[/block]\nPlease note that if `/usr/local/share/man` is not in your manpath then you should use any other directory from the manpath such as:\n\n  * `/usr/local/man`\n  * `/usr/share/man`\n\n##macOS\n\n##Prerequisite\n\nBefore installing SBFS, please install [FUSE for macOS](https://osxfuse.github.io/). Check if FUSE is installed via your **System Preferences**. \n\n###Procedure\n\n1. Download the [SBFS executable file](https://static.sbgenomics.com/sbfs/linux-amd64/sbfs).\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"curl https://igor.sbgenomics.com/downloads/sbfs/darwin-amd64/sbfs -O\",\n      \"language\": \"text\",\n      \"name\": \"Downloading the SBFS\"\n    }\n  ]\n}\n[/block]\n 2. Change the file permissions so you are able to run the executable.\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"chmod a+x sbfs\",\n      \"language\": \"text\",\n      \"name\": \"Changing the file permissions\"\n    }\n  ]\n}\n[/block]\n The SBFS is now fully installed. See below for optional SBFS operations. \n\n\n###Optional operations\n\n####Add SBFS to the PATH\n\nAdd SBFS to the PATH to facilitate performing all SBFS operations using one of the following methods. Note that this is an optional step as the SBFS is also available if you provide the full path to the executable (e.g. `path/to/dir/sbfs`).\n\n* **Move SBFS binary** to a directory which is already in the PATH.\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"sudo mv sbfs /usr/local/bin/\",\n      \"language\": \"text\",\n      \"name\": \"Adding SBFS to the PATH\"\n    }\n  ]\n}\n[/block]\n* **Add the directory** which contains SBFS to the PATH. You can also create either a hard link or a symbolic link to the SBFS binary. \n\n####Add bash completion for SBFS\n\nPlease note that this only works with bash completion version 4, which should be previously installed and enabled.\n\nTo add bash completion on macOS, issue the following command: \n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"sudo bash -c \\\"sbfs gen completion > /usr/local/etc/bash_completion.d/sbfs\",\n      \"language\": \"text\",\n      \"name\": \"Adding bash completion\"\n    }\n  ]\n}\n[/block]\nTo complete enabling SBFS bash completion restart the terminal application or source SBFS bash completion while staying in the same terminal application with this command:\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"source /usr/local/etc/bash_completion.d/sbfs\",\n      \"language\": \"text\",\n      \"name\": \"Adding bash completion\"\n    }\n  ]\n}\n[/block]\n \n####Install man pages\n\nTo install `man` pages, use this command:\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"sudo sbfs gen man /usr/local/share/man/man1/\",\n      \"language\": \"text\",\n      \"name\": \"Installing man pages\"\n    }\n  ]\n}\n[/block]\nPlease note that if `/usr/local/share/man` is not in your `manpath` then you should use any other directory from the `manpath` such as :\n \n  * `/usr/local/man`\n  * `/usr/share/man`","excerpt":"","slug":"install-sbfs-manually","type":"basic","title":"Install SBFS manually"}

Install SBFS manually


##Overview Install SBFS manually for Linux and macOS. Note that these instructions are meant for advanced users. Conversely, learn to [install SBFS automatically](doc:install-sbfs-automatically). ###Linux 1. Download the [SBFS executable file](https://static.sbgenomics.com/sbfs/linux-amd64/sbfs). [block:code] { "codes": [ { "code": "curl https://igor.sbgenomics.com/downloads/sbfs/linux-amd64/sbfs -O", "language": "text", "name": "Downloading the SBFS" } ] } [/block] 2. Change the file permissions so you are able to run the executable [block:code] { "codes": [ { "code": "chmod a+x sbfs", "language": "text", "name": "Changing the permissions" } ] } [/block] The SBFS is now fully installed. See below for optional SBFS operations. ###Optional operations ####Add SBFS to the PATH Add SBFS to the PATH to facilitate performing all SBFS operations using one of the following methods. Note that this is an optional step as the SBFS is also available if you provide the full path to the executable (e.g. `path/to/dir/sbfs`). * **Move SBFS binary** to a directory which is already in the PATH. [block:code] { "codes": [ { "code": "sudo mv sbfs /usr/local/bin/", "language": "text", "name": "Moving the SBFS binary" } ] } [/block] * **Add the directory** which contains SBFS to the PATH. You can also create either a hard link or a symbolic link to the SBFS binary. ####Add bash completion for SBFS Please note that this only works with bash completion version 4, which should be previously installed and enabled. To add bash completion on Linux, issue the following command: [block:code] { "codes": [ { "code": "sudo bash -c \"sbfs gen completion > /etc/bash_completion.d/sbfs\"", "language": "text", "name": "Adding bash completion on Linux" } ] } [/block] To complete enabling SBFS bash completion restart the terminal application or source SBFS bash completion while staying in the same terminal application with this command: [block:code] { "codes": [ { "code": "sudo sbfs gen man /usr/local/share/man/man1/", "language": "text", "name": "Enable the bash completion" } ] } [/block] Please note that if `/usr/local/share/man` is not in your manpath then you should use any other directory from the manpath such as: * `/usr/local/man` * `/usr/share/man` ##macOS ##Prerequisite Before installing SBFS, please install [FUSE for macOS](https://osxfuse.github.io/). Check if FUSE is installed via your **System Preferences**. ###Procedure 1. Download the [SBFS executable file](https://static.sbgenomics.com/sbfs/linux-amd64/sbfs). [block:code] { "codes": [ { "code": "curl https://igor.sbgenomics.com/downloads/sbfs/darwin-amd64/sbfs -O", "language": "text", "name": "Downloading the SBFS" } ] } [/block] 2. Change the file permissions so you are able to run the executable. [block:code] { "codes": [ { "code": "chmod a+x sbfs", "language": "text", "name": "Changing the file permissions" } ] } [/block] The SBFS is now fully installed. See below for optional SBFS operations. ###Optional operations ####Add SBFS to the PATH Add SBFS to the PATH to facilitate performing all SBFS operations using one of the following methods. Note that this is an optional step as the SBFS is also available if you provide the full path to the executable (e.g. `path/to/dir/sbfs`). * **Move SBFS binary** to a directory which is already in the PATH. [block:code] { "codes": [ { "code": "sudo mv sbfs /usr/local/bin/", "language": "text", "name": "Adding SBFS to the PATH" } ] } [/block] * **Add the directory** which contains SBFS to the PATH. You can also create either a hard link or a symbolic link to the SBFS binary. ####Add bash completion for SBFS Please note that this only works with bash completion version 4, which should be previously installed and enabled. To add bash completion on macOS, issue the following command: [block:code] { "codes": [ { "code": "sudo bash -c \"sbfs gen completion > /usr/local/etc/bash_completion.d/sbfs", "language": "text", "name": "Adding bash completion" } ] } [/block] To complete enabling SBFS bash completion restart the terminal application or source SBFS bash completion while staying in the same terminal application with this command: [block:code] { "codes": [ { "code": "source /usr/local/etc/bash_completion.d/sbfs", "language": "text", "name": "Adding bash completion" } ] } [/block] ####Install man pages To install `man` pages, use this command: [block:code] { "codes": [ { "code": "sudo sbfs gen man /usr/local/share/man/man1/", "language": "text", "name": "Installing man pages" } ] } [/block] Please note that if `/usr/local/share/man` is not in your `manpath` then you should use any other directory from the `manpath` such as : * `/usr/local/man` * `/usr/share/man`