[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"detail-sidebar-cat-1-en-105":3,"doc-seo-573362-105":53,"doc-detail-573362-en":126},{"code":4,"msg":5,"data":6},0,"success",[7,14,19,24,29,34,39,44,49],{"id":8,"doc_module":9,"doc_module_name":10,"category_name":11,"show_sort_weight":12,"slug":13},11,1,"Template","Presentations",90,"presentations",{"id":15,"doc_module":9,"doc_module_name":10,"category_name":16,"show_sort_weight":17,"slug":18},12,"Resumes",80,"resumes",{"id":20,"doc_module":9,"doc_module_name":10,"category_name":21,"show_sort_weight":22,"slug":23},14,"Invoices",70,"invoices",{"id":25,"doc_module":9,"doc_module_name":10,"category_name":26,"show_sort_weight":27,"slug":28},15,"Posters",60,"posters",{"id":30,"doc_module":9,"doc_module_name":10,"category_name":31,"show_sort_weight":32,"slug":33},16,"Social Media",50,"social-media",{"id":35,"doc_module":9,"doc_module_name":10,"category_name":36,"show_sort_weight":37,"slug":38},17,"Forms",40,"forms",{"id":40,"doc_module":9,"doc_module_name":10,"category_name":41,"show_sort_weight":42,"slug":43},18,"Letters",30,"letters",{"id":45,"doc_module":9,"doc_module_name":10,"category_name":46,"show_sort_weight":47,"slug":48},21,"Paper Templates",5,"papers-templates",{"id":50,"doc_module":9,"doc_module_name":10,"category_name":51,"show_sort_weight":4,"slug":52},158,"General","general-158",{"code":4,"msg":54,"data":55},"ok",{"site_id":56,"language":57,"slug":58,"title":59,"keywords":60,"description":61,"schema_data":62,"social_meta":119,"head_meta":121,"extra_data":123,"updated_unix":125},105,"en","linux-beyond-the-basics-oct-2022-hot-topics","Linux - Beyond the Basics - Oct. 2022 Hot Topics","","Guide to logging in and working on Linux servers for bioinformatics and research computing, using MIT Whitehead Institute/BaRC Hot Topics (Oct. 2022). Covers creating a training working directory, copying exercise files, connecting to tak/fry via ssh and terminal (Windows via MobaXterm, macOS via Terminal), and submitting large commands to LSF and Slurm using bsub/sbatch with job monitoring (bjobs/squeue) and output retrieval. Reviews essential Linux commands, common mistakes like case sensitivity and spaces, handling DOS carriage returns, and using pipes. Introduces topics for further discussion: aliases, sed, awk, join, bedtools, loops, and scripting.",{"@graph":63,"@context":118},[64,80,101],{"@type":65,"itemListElement":66},"BreadcrumbList",[67,71,74,77],{"item":68,"name":69,"@type":70,"position":9},"https://docshare.wps.com","Home","ListItem",{"item":72,"name":10,"@type":70,"position":73},"https://docshare.wps.com/template/",2,{"item":75,"name":11,"@type":70,"position":76},"https://docshare.wps.com/template/presentations/",3,{"item":78,"name":59,"@type":70,"position":79},"https://docshare.wps.com/template/linux-beyond-the-basics-oct-2022-hot-topics/573362/",4,{"url":78,"name":59,"@type":81,"image":82,"author":87,"headline":59,"publisher":90,"fileFormat":93,"inLanguage":57,"description":61,"dateModified":94,"datePublished":95,"encodingFormat":93,"isAccessibleForFree":96,"interactionStatistic":97},"DigitalDocument",{"url":83,"@type":84,"width":85,"height":86},"https://docshare.wps.com/thumbnails/linux-beyond-the-basics-oct-2022-hot-topics/573362.png","ImageObject",442,249,{"name":88,"@type":89},"Eliana","Person",{"url":68,"name":91,"@type":92},"DocShare","Organization","application/pdf","2026-10-18","2026-10-14",true,{"@type":98,"interactionType":99,"userInteractionCount":76},"InteractionCounter",{"@type":100},"ViewAction",{"@type":102,"mainEntity":103},"FAQPage",[104,110,114],{"name":105,"@type":106,"acceptedAnswer":107},"How do you request a tak/fry account and what should you do after logging in?","Question",{"text":108,"@type":109},"Request a tak/fry account via the provided unixRequest link. After logging in to tak, create a directory under your home directory (e.g., mkdir Hot_Topics), use it as the working directory, and prepare the exercise files there.","Answer",{"name":111,"@type":106,"acceptedAnswer":112},"How can you run and monitor batch commands on the LSF and Slurm clusters?",{"text":113,"@type":109},"For LSF, submit with bsub (example shown with sleep/pwd/ls) and check status with bjobs -w, then inspect with bpeek \u003CjobID>. For Slurm, submit with sbatch including partition, jobname, memory, and a wrapped command, then monitor with squeue and read outputs from slurm-*out.",{"name":115,"@type":106,"acceptedAnswer":116},"What common Linux pitfalls are highlighted in the Linux review?",{"text":117,"@type":109},"Key mistakes include case sensitivity in directory paths, spaces affecting commands (e.g., rm patterns), and text encoding or typography issues from office software such as smart quotes/dashes or DOS carriage returns, which can be removed with fromdos.","https://schema.org",{"og:url":78,"og:type":120,"og:title":59,"og:site_name":91,"og:description":61},"article",{"robots":122,"canonical":78},"index,follow",{"doc_id":124,"site_id":56},573362,1792242027,{"code":4,"msg":5,"data":127},{"doc_id":124,"user_id":128,"nickname":88,"user_avatar":129,"doc_module":9,"category_id":8,"category_name":11,"doc_title":59,"doc_description":61,"doc_content":130,"file_id":131,"file_url":132,"file_type":133,"file_size":134,"view_count":76,"is_deleted":4,"is_public":9,"is_downloadable":9,"audit_status":9,"page_count":135,"language":136,"language_code":57,"site_id":56,"html_lang":57,"table_of_contents":137,"faqs":138,"seo_title":139,"seo_description":61,"update_tm":140,"read_time":8},4398048949847,"https://ap-avatar.wpscdn.com/avatar/400002536579ef2da7f?_k=1778318612642679267","Linux: Beyond the Basics  \nBingbing Yuan and George Bell  \nBaRC Hot Topics – Oct. 2022  \nBioinformatics and Research Computing  \nWhitehead Institute  \n[http://barc.wi.mit.edu/hot_topics/](http://barc.wi.mit.edu/hot_topics/)  \nLogging in to our Linux servers  \n• Our main Linux servers are tak and fry fry has the most up‐to‐date software  \n• Request a tak/fry account:  \n[https://element.wi.mit.edu/am/?f=unixRequest](https://element.wi.mit.edu/am/?f=unixRequest)  \n• Connecting to tak or fry:  \n[http://bioinfo.wi.mit.edu/bio/software/unix/serverConnect.php](http://bioinfo.wi.mit.edu/bio/software/unix/serverConnect.php)  \n– Windows:  \n􀂾 MobaXterm  \n– Mac  \n􀂾 Access through Terminal  \n2  \nLog in to tak for Mac  \nssh –[Y username@tak.wi.mit.edu](Y username@tak.wi.mit.edu)  \n3  \nConnecting to tak from Windows  \n1) Open MobaXterm  \n2) Click on the ”Start local terminal” button  \n3) Type:  \nssh -Y [username@tak.wi.mit.edu](username@tak.wi.mit.edu)  \nNote:  \nWhen you write the password you won’t se any characters being typed.  \nSending big commands to the cluster   \nWhat does this command do?  \n\\# Send command from tak to lsf cluster  \nbsub \"sleep 100; pwd; ls -l\"  \n\\# Check in progress status  \nbjobs –w  \nbpeek \u003CjobID>  \n\\# Read command output => check email  \n\\# Send command from fry to slurm cluster  \nsbatch --partition=20 --jobname=HT_TEST --mem=4G --wrap\"sleep 100; pwd; ls -l\"  \n\\# Check in‐progress status  \nsqueue  \ncat slurm-*out  \n\\# Get command output => read slurm‐*out  \nHot Topics website: [http://barc.wi.mit.edu/education/hot_topics/](http://barc.wi.mit.edu/education/hot_topics/)  \n• After you login to tak, create a directory for the exercises within your home directory, and use it as your working directory $ mkdir Hot_Topics  \n$ cd Hot_Topics  \n• Copy all files into your working directory $ cp ‐r /nfs/BaRC_training/Linux_Beyond/data_files/* .  \n• You should have the files below in your working directory:  \n• datasets/ Ensembl_info.txt exercise.txt foo.txt Gene_exp.txt HumanGenes PlusMinus3kb.bed peaks.bed sample1.txt exercise.pdf  \n– You can check they’re there with one of these commands:  \n• ls  \n• find  \n6  \nLinux Review:  \nCommands  \n􀂾 command [arg1 arg2 … ] [input1 input2 … ]  \n$ sort ‐k2,[3nr foo.tab](3nr foo.tab)  \n‐n or ‐g: ‐n  \nstart end  \na  \nis recommended, except for scientific notation or leading '+'  \n‐r: reverse order  \n$ cut ‐f1,5 [foo.tab](foo.tab)  \n$ cut ‐f1‐5 [foo.tab](foo.tab)  \n‐f: select only these fields  \n‐f1,5: select 1st and 5th fields  \n‐f1‐5: select 1st, 2 nd, 3 rd, 4th, and 5th fields  \n$ wc ‐l foo.txt  \nHow many lines are in this file?  \n7  \nLinux Review: Common Mistakes  \n• Case sensitive  \ncd /nfs/Barc_Public is different from cd /nfs/BaRC_Public  \n-bash: cd: /nfs/Barc_Public: No such file or directory  \n• Spaces may matter!  \nrm –f myFiles* vs rm –f myFiles *  \n• Office applications can convert text to special characters that Linux won’t understand  \n• Smart quotes, dashes  \n• Carriage return from DOS  \n– Use fromdos to remove carriage return  \n8  \nLinux Review: Pipes  \n• Stream output of one command/program as input for another  \n– Avoid intermediate file(s)  \n– Merge multiple commands in to one long command  \n􀂾 $ cut ‐f1 myFile.txt | sort | uniq ‐c > uniqCounts.txt  \n pipes   \n9  \nWhat we will discuss today  \n• Aliases (to reduce typing)  \n• sed (for file manipulation)  \n• awk(to filter by column)  \n• join (merge files)  \n• groupBy and intersect from bedtools (not typical Linux)  \n• loops (one‐line and with shell scripts)  \n• scripting (to streamline commands)  \n10","cbCail93YXc8Jju2","https://ap.wps.com/l/cbCail93YXc8Jju2","pdf",1244938,31,"English","# Logging in to our Linux servers\n## Requesting accounts and connecting to tak/fry\n## Login commands for macOS and Windows\n# Sending big commands to the cluster\n## LSF (bsub) workflow and monitoring\n## Slurm (sbatch) workflow and monitoring\n## Reading outputs\n# Linux Review: Commands\n## sort, cut, wc\n# Linux Review: Common Mistakes\n## case sensitivity, spaces, special characters\n# Linux Review: Pipes\n## piping examples\n# What we will discuss today\n## aliases, sed, awk, join, loops, scripting","[{\"question\":\"How do you request a tak/fry account and what should you do after logging in?\",\"answer\":\"Request a tak/fry account via the provided unixRequest link. After logging in to tak, create a directory under your home directory (e.g., mkdir Hot_Topics), use it as the working directory, and prepare the exercise files there.\"},{\"question\":\"How can you run and monitor batch commands on the LSF and Slurm clusters?\",\"answer\":\"For LSF, submit with bsub (example shown with sleep/pwd/ls) and check status with bjobs -w, then inspect with bpeek \\u003cjobID\\u003e. For Slurm, submit with sbatch including partition, jobname, memory, and a wrapped command, then monitor with squeue and read outputs from slurm-*out.\"},{\"question\":\"What common Linux pitfalls are highlighted in the Linux review?\",\"answer\":\"Key mistakes include case sensitivity in directory paths, spaces affecting commands (e.g., rm patterns), and text encoding or typography issues from office software such as smart quotes/dashes or DOS carriage returns, which can be removed with fromdos.\"}]","Linux - Beyond the Basics - Oct. 2022 Hot Topics | PDF",1791938012]