Last login: Wed Mar 29 17:04:39 on ttys000 iMac-2:~ yen-yiho$ #################################################################################### ## Connect to Maxwell #################################################################################### iMac-2:~ yen-yiho$ ssh -p 222 hoyen@login.rci.sc.edu Password: Duo two-factor login for hoyen Enter a passcode or select one of the following options: 1. Duo Push to XXX-XXX-3068 2. Phone call to XXX-XXX-3068 3. SMS passcodes to XXX-XXX-3068 Passcode or option (1-3): 1 Pushed a login request to your device... Success. Logging you in... [hoyen@maxwell ~]$ ls [hoyen@sms ~]$ module avail ------------------------------- /usr/share/Modules/modulefiles -------------------------------- bowtie2/2.3.1 module-info opt-python rocks-openmpi_ib dot modules python/anaconda2.4 use.own gcc/4.9.3 mpich2-x86_64 rna-star/2.5.2 module-git null rocks-openmpi -------------------------------------- /etc/modulefiles --------------------------------------- openmpi-x86_64 ------------------------------- /share/apps/Modules/modulefiles ------------------------------- bowtie2/2.3.1 modules R/3.1.2 star-2.5.2 dot mpich2-x86_64 R/3.3.0 use.own gcc/4.9.3 null rna-star/2.5.2 module-git opt-python rocks-openmpi module-info python/anaconda2.4 rocks-openmpi_ib [hoyen@maxwell ~]$ ls [hoyen@maxwell ~]$ cd ncbi [hoyen@maxwell ncbi]$ cd .. [hoyen@maxwell ~]$ [hoyen@maxwell ~]$ [hoyen@maxwell ~]$ [hoyen@maxwell ~]$ ls Aligned.out.sam chip_1_1.fq Log.out ncbi _STARtmp bin chip.fastq Log.progress.out Rlibs bio Lab16.R mydata.csv SRR002320.fastq [hoyen@maxwell ~]$ cd ncbi [hoyen@maxwell ncbi]$ ls public [hoyen@maxwell ncbi]$ cd public [hoyen@maxwell public]$ ls aligned fastq sra [hoyen@maxwell public]$ [hoyen@maxwell public]$ cd ~ [hoyen@maxwell ~]$ ls Aligned.out.sam chip_1_1.fq Log.out ncbi _STARtmp bin chip.fastq Log.progress.out Rlibs bio Lab16.R mydata.csv SRR002320.fastq [hoyen@maxwell ~]$ rm mydata.csv [hoyen@maxwell ~]$ rm Lab16.R [hoyen@maxwell ~]$ [hoyen@maxwell ~]$ [hoyen@maxwell ~]$ ls Aligned.out.sam bio chip.fastq Log.progress.out Rlibs _STARtmp bin chip_1_1.fq Log.out ncbi SRR002320.fastq [hoyen@maxwell ~]$ [hoyen@maxwell ~]$ mkdir test [hoyen@maxwell ~]$ ls Aligned.out.sam bio chip.fastq Log.progress.out Rlibs _STARtmp bin chip_1_1.fq Log.out ncbi SRR002320.fastq test [hoyen@maxwell ~]$ rm -rf test [hoyen@maxwell ~]$ ls Aligned.out.sam bio chip.fastq Log.progress.out Rlibs _STARtmp bin chip_1_1.fq Log.out ncbi SRR002320.fastq [hoyen@maxwell ~]$ [hoyen@maxwell ~]$ module avail R --------------------------- /share/apps/Modules/modulefiles ---------------------------- R/3.1.2 R/3.3.0 [hoyen@maxwell ~]$ module load R/3.1.2 [hoyen@maxwell ~]$ R R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-unknown-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > > q() Save workspace image? [y/n/c]: n [hoyen@maxwell ~]$ [hoyen@maxwell ~]$ mkdir Rlibs [hoyen@maxwell ~]$ ls Aligned.out.sam bio chip.fastq Log.progress.out Rlibs _STARtmp bin chip_1_1.fq Log.out ncbi SRR002320.fastq [hoyen@maxwell ~]$ module load R/3.1.2 [hoyen@maxwell ~]$ R #################################################################################### ## In R #################################################################################### R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-unknown-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > > > .libPaths("~/Rlibs") > > > source("http://www.bioconductor.org/biocLite.R") Bioconductor version 3.0 (BiocInstaller 1.16.5), ?biocLite for help A new version of Bioconductor is available after installing the most recent version of R; see http://bioconductor.org/install > > > biocLite("ALL") > data(ALL) Warning message: In data(ALL) : data set 'ALL' not found > > library(ALL) > > data(ALL) > > dim(ALL) Features Samples 12625 128 > > q() Save workspace image? [y/n/c]: n #################################################################################### ## Get a file from a website #################################################################################### [hoyen@maxwell ~]$ wget http://people.stat.sc.edu/hoyen/BIOL599/RCode/Lab16.R [hoyen@maxwell ~]$ ls #################################################################################### ## View a text file #################################################################################### [hoyen@maxwell ~]$ more SRR002320.fastq [hoyen@maxwell ~]$ exit