{"id":16319393,"url":"https://github.com/lcolladotor/config_jhpce","last_synced_at":"2025-10-03T15:45:45.521Z","repository":{"id":149808641,"uuid":"208142198","full_name":"lcolladotor/config_jhpce","owner":"lcolladotor","description":"My JHPCE configuration files","archived":false,"fork":false,"pushed_at":"2019-09-18T18:43:33.000Z","size":31,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-02-16T22:44:46.415Z","etag":null,"topics":["bash","rprofile","rstats","sge","sge-cluster"],"latest_commit_sha":null,"homepage":"","language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/lcolladotor.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-09-12T20:37:45.000Z","updated_at":"2019-09-18T18:43:35.000Z","dependencies_parsed_at":null,"dependency_job_id":"6f63bb04-3553-475f-ae6d-31a0b606e0a9","html_url":"https://github.com/lcolladotor/config_jhpce","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lcolladotor%2Fconfig_jhpce","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lcolladotor%2Fconfig_jhpce/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lcolladotor%2Fconfig_jhpce/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lcolladotor%2Fconfig_jhpce/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lcolladotor","download_url":"https://codeload.github.com/lcolladotor/config_jhpce/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":254044959,"owners_count":22005264,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bash","rprofile","rstats","sge","sge-cluster"],"created_at":"2024-10-10T22:26:47.428Z","updated_at":"2025-10-03T15:45:40.501Z","avatar_url":"https://github.com/lcolladotor.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# JHPCE config files\n\nHere are some of my [JHPCE](https://jhpce.jhu.edu/) configuration files.\n\n## bashrc\n\nMy `~/.bashrc` file:\n\n\n```bash\n# .bashrc\n\n# Source global definitions\nif [ -f /etc/bashrc ]; then\n\t. /etc/bashrc\nfi\n\n# User specific aliases and functions\n# Auto-complete command from history\n# http://lindesk.com/2009/04/customize-terminal-configuration-setting-bash-cli-power-user/\nexport INPUTRC=~/.inputrc\n# http://www.biostat.jhsph.edu/~afisher/ComputingClub/webfiles/KasperHansenPres/IntermediateUnix.pdf\n# https://unix.stackexchange.com/questions/48713/how-can-i-remove-duplicates-in-my-bash-history-preserving-order\nexport HISTCONTROL=ignoreboth:erasedups\nexport HISTSIZE=20000\nshopt -s histappend\nshopt -s cmdhist\n\n# http://superuser.com/questions/384769/alias-rm-rm-i-considered-harmful\nalias rmi='rm -i'\n\n# Change command prompt\n# http://www.cyberciti.biz/tips/howto-linux-unix-bash-shell-setup-prompt.html\n# http://www.cyberciti.biz/faq/bash-shell-change-the-color-of-my-shell-prompt-under-linux-or-unix/\n# https://bbs.archlinux.org/viewtopic.php?id=48910\n# previous in enigma2: \"[\\u@\\h \\W]\\$ \"\n# previously in mac: \"\\h:\\W \\u\\$ \"\nexport PS1=\"\\[\\e[0;33m\\]\\A \\W \\$ \\[\\e[m\\]\"\n\n# ascp (Aspera Connect) http://downloads.asperasoft.com/en/downloads/8?list\n#export PATH=~/.aspera/connect/bin/:$PATH\n\n# Amber2 scracth space (not backed up) for file storage.\nalias amber2=\"cd /legacy/amber2/scratch/lcollado/\"\n\n# Brain data results by Alyssa\nalias brain=\"cd /legacy/amber2/scratch/jleek/orbFrontal/results/\"\nalias stanley=\"cd /dcs01/stanley/work/brain_rna/\"\n\n# LIDB BRAIN projects\nalias libd=\"cd /legacy/nexsan2/disk3/ajaffe/RNASeq/BRAIN/\"\nalias dersold=\"cd /dcs01/ajaffe/Brain/derRuns/\"\nalias ders=\"cd /dcl01/lieber/ajaffe/derRuns/\"\nalias jaffe=\"cd /dcl01/lieber/ajaffe\"\nalias labold=\"cd /dcl01/lieber/ajaffe/lab\"\nalias lab=\"cd /dcl01/ajaffe/data/lab\"\nalias emily=\"cd /dcl01/lieber/ajaffe/Emily\"\nalias rna=\"cd /dcl01/lieber/ajaffe/Emily/RNAseq-pipeline/sh\"\n\n## RNA-seq mapping bias\n#alias mapbias=\"cd /dcs01/ajaffe/mapBias\"\n\n## Leekgroup luster dir\nalias leek=\"cd /dcl01/leek/data/\"\nalias recount=\"cd /dcl01/leek/data/recount-website\"\nalias recounta=\"cd /dcl01/leek/data/recount-analyses\"\nalias recount2=\"cd /dcl01/leek/data/gtex_work/runs/recount2\"\n\n## Pandey's recount resoults\nalias pandey=\"cd /dcl01/leek/data/recount_pandey\"\nalias panday-raw=\"cd /dcl01/leek/data/sunghee_analysis/processed\"\n\n## Creating modules\n# https://lmod.readthedocs.io/en/latest/050_lua_modulefiles.html\nalias modsrc=\"cd /jhpce/shared/jhpce/libd\"\nalias modlua=\"cd /jhpce/shared/jhpce/modulefiles/libd\"\n\n# colors\n# http://norbauer.com/notebooks/code/notes/ls-colors-and-terminal-app\n# used BSD pattern ExGxFxDxBxEgEdxbxgxhxd on http://geoff.greer.fm/lscolors/\n# that tool does not specify the colors, which I did by looking manually at\n# http://blog.twistedcode.org/2008/04/lscolors-explained.html\n# and the norbauer.com site previously mentioned\nalias ls=\"ls --color=auto\"\n#export LS_COLORS=\"di=1;34;40:ln=1;36;40:so=1;35;40:pi=1;93;40:ex=1;31;40:bd=1;34;46:cd=1;34;43:su=0;41:sg=0;46:tw=0;47:ow=0;43\"\n## After switching to RStudio:\n# https://askubuntu.com/questions/466198/how-do-i-change-the-color-for-directories-with-ls-in-the-console\nexport LS_COLORS=\"di=0;32:ln=0;36:so=0;35:pi=0;93:ex=0;31:bd=0;34;46:cd=0;34;43:su=0;41:sg=0;46:tw=0;47:ow=0;43:fi=0;33\"\n\n# Uncomment below for Mac and comment the two previous commands\n#export CLICOLOR=1\n#export LSCOLORS=\"ExGxFxDxBxEgEdxbxgxhxd\"\n\n## Python\n#export PYTHONPATH=\"/users/lcollado/.local/lib/python2.7/site-packages/\"\n#export PYTHONPATH=/users/lcollado/python/python2.7.9:/jhpce/shared/community/compiler/gcc/4.4.7/python/2.7.9/lib/python2.7\n#export PATH=/users/lcollado/software/localpython/bin:$PATH\n\n## change dir automatically when using qrsh\n## Details: https://github.com/rkostadi/BiocHopkins/wiki/Useless-Tips-\u0026-Code-Snippets\nif [ -f ~/.bash_pwd ]; then\n    source ~/.bash_pwd\n    rm ~/.bash_pwd\nfi\nalias qr='echo \"cd $PWD\" \u003e ~/.bash_pwd; history -w; qrsh'\n#alias qr='export LEODIR=`pwd`; history -w \u0026\u0026 qrsh -ac LEODIR'\n#alias qr='echo \"hola\"'\n\n## For setup:\n# http://erniemiller.org/2011/12/12/textmate-2-rmate-awesome/\n## For laptop config:\n# http://jonsimpson.co.uk/log/2011/rmate-ssh-remoteforward\n## rmate port\n# https://github.com/textmate/rmate\nexport RMATE_PORT=\"_a_five_digit_number_\"\n\n## For remotes::install_github()\nexport GITHUB_PAT=\"something_here\"\n\n## Load the git module by default when qrsh/qsub\n## thanks to Jiong Yang\nif [[ $HOSTNAME == compute-* ]]; then\n    echo \"Adding LIBD modules\"\n    module use /jhpce/shared/jhpce/modulefiles/libd\n    echo \"Loading git\"\n    module load git\n    module load git-status-size/github\n    # module load git-lfs/2.8.0\n    module load rmate/1.5.9\n    module load conda_R/3.6\nfi\n\n## To deal with running nextflow without requesting much more memory\n## https://jhpce.jhu.edu/question/why-do-i-get-memory-errors-when-running-java/\nexport _JAVA_OPTIONS=\"-Xms5g -Xmx6g\"\n\n```\n\n## `input_rc`\n\nMy `~/.input_rc` file:\n\n```bash\n#Page up/page down\n\"\\e[B\": history-search-forward\n\"\\e[A\": history-search-backward\n\n$include /etc/inputrc\n\n```\n\n## `sge_request`\n\nMy `~/.sge_request` file:\n\n```bash\n# Check http://www.biostat.jhsph.edu/bit/cluster-usage.html for more instructions\n#\n# Set defaults for mem_free and h_vmem\n-l mem_free=12G,h_vmem=12G\n#\n# Set the standard value for stack size limit\n# (needed for some programs to run properly when h_vmem is set)\n-l h_stack=512M\n#\n# Set a default maximum file size that an SGE job can create\n-l h_fsize=100G\n# Define my email\n-M fellgernon@gmail.com\n# To get an email on a job use -m e\n\n```\n\n## `gitconfig`\n\nMy `.gitconfig` file:\n\n```\n[user]\n\tname = lcolladotor\n\temail = lcollado@jhsph.edu\n[alias]\n\tco = checkout\n\tbr = branch\n\tci = commit\n\tst = status\n[http]\n\tsslVerify = false\n[core]\n\texcludesfile = /users/lcollado/.gitignore_global\n[filter \"lfs\"]\n\tclean = git-lfs clean -- %f\n\tsmudge = git-lfs smudge -- %f\n\tprocess = git-lfs filter-process\n\trequired = true\n\n```\n\nMy `~/.gitignore_global` file:\n\n```\n*~\n\n## More at\n## https://help.github.com/articles/ignoring-files\n\n# R history #\n#############\n.Rapp.history\n.Rhistory\n\n# LaTeX stuff #\n###############\n*.aux\n*.out\n\n\n# Compiled source #\n###################\n*.com\n*.class\n*.dll\n*.exe\n*.o\n*.so\n\n# Packages #\n############\n# it's better to unpack these files and commit the raw source\n# git has its own built in compression methods\n*.7z\n*.dmg\n*.gz\n*.iso\n*.jar\n*.rar\n*.tar\n*.zip\n\n# Logs and databases #\n######################\n*.log\n*.sql\n*.sqlite\n\n# OS generated files #\n######################\n.DS_Store\n.DS_Store?\n._*\n.Spotlight-V100\n.Trashes\nIcon?\nehthumbs.db\nThumbs.db\n```\n\n## `Rprofile`\n\nMy `~/.Rprofile` file:\n\n```R\n## Change colors\n# Source https://github.com/jalvesaq/colorout\nif(Sys.getenv('TERM') %in% c(\"term\", \"xterm-256color\", \"cygwin\", \"screen\") \u0026 interactive()) {\n\tinstalled \u003c- require(\"colorout\")\n\tif(!installed) {\n\t\tcat('devtools::install_github(\"jalvesaq/colorout\")\\n')\n\t}\n\trm(installed)\n\n    ## rmote for images\n    # https://github.com/cloudyr/rmote\n    # https://community.rstudio.com/t/feature-request-send-plots-from-r-in-terminal-to-plots-pane/1877/3\n    installed \u003c- require('rmote')\n    if(!installed) {\n        cat('install.packages(\"rmote\", repos = c(CRAN = \"http://cran.rstudio.com\",\n  tessera = \"http://packages.tessera.io\"))')\n    } else {\n        start_rmote(port = _another_five_digit_number_, server_dir = paste0('/users/lcollado/rmote/rmote_server_', Sys.Date()))\n    }\n    rm(installed)\n}\n\n#library('fcuk')\n\n# https://bookdown.org/yihui/blogdown/global-options.html\noptions(blogdown.author = 'L. Collado-Torres')\noptions(blogdown.ext = '.Rmd')\n\n## https://blog.rstudio.com/2013/06/10/rstudio-cran-mirror/\noptions(repos = c(CRAN = \"https://cran.rstudio.com\"))\n\n```\n\n## `ssh`\n\nMy `~/.ssh/config` file:\n\n```bash\n# For rmate\nHost compute*\n    RemoteForward _a_five_digit_number_ localhost:_a_five_digit_number_\n    LocalForward _another_five_digit_number_ localhost:_another_five_digit_number_\n\n# Default GitHub user\nHost github.com\n    HostName github.com\n    PreferredAuthentications publickey\n    IdentityFile ~/.ssh/id_rsa\n\n# Work user account\nHost bitbucket.org\n    HostName bitbucket.org\n    PreferredAuthentications publickey\n    IdentityFile ~/.ssh/id_rsa\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flcolladotor%2Fconfig_jhpce","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flcolladotor%2Fconfig_jhpce","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flcolladotor%2Fconfig_jhpce/lists"}