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2020_Bioinformatics_Research_Experience

Base repository for Coriell Institute's inaugural Bioinformatics Research Experience

Command Line Options for Transferring Files

Because MacOS Catalina is too secure

Secure File Transfer Protocol (SFTP)

This logs you into the server, similarly to ssh so you can look around and navigate the filesystem, and allows to upload and download files. In addition to what I show below, there’s a helpful list of commands at the link https://www.uppmax.uu.se/support/user-guides/basic-sftp-commands/

Logging In

To get started, log in to the server using sftp instead of ssh

### log in using sftp instead of ssh
sftp kkeith@10.1.105.13

Downloading

To transfer stuff from your local (personal) computer to the server, use the command get. This is what you’ll primarily need to do for the rest of the experience.

### EXAMPLE: tranfer stuff from the server to your machine
# look around on the server
sftp> ls
data              rnaseq_practice
# go to the folder you want to grab stuff from
sftp> cd rnaseq_practice/data/fastqc
sftp> ls
ls
dac1_chr21_R1_fastqc.html  dac1_chr21_R1_fastqc.zip   dac1_chr21_R2_fastqc.html  dac1_chr21_R2_fastqc.zip   
dac2_chr21_R1_fastqc.html  dac2_chr21_R1_fastqc.zip   dac2_chr21_R2_fastqc.html  dac2_chr21_R2_fastqc.zip   
dac3_chr21_R1_fastqc.html  dac3_chr21_R1_fastqc.zip   dac3_chr21_R2_fastqc.html  dac3_chr21_R2_fastqc.zip   
siC1_chr21_R1_fastqc.html  siC1_chr21_R1_fastqc.zip   siC1_chr21_R2_fastqc.html  siC1_chr21_R2_fastqc.zip   
siC2_chr21_R1_fastqc.html  siC2_chr21_R1_fastqc.zip   siC2_chr21_R2_fastqc.html  siC2_chr21_R2_fastqc.zip   
siC3_chr21_R1_fastqc.html  siC3_chr21_R1_fastqc.zip   siC3_chr21_R2_fastqc.html  siC3_chr21_R2_fastqc.zip
# download all the html files
sftp> get *.html
Fetching /home/kkeith/rnaseq_practice/data/fastqc/dac1_chr21_R1_fastqc.html to dac1_chr21_R1_fastqc.html
/home/kkeith/rnaseq_practice/data/fastqc/dac1_chr21_R1_fastqc.html         100%  243KB  33.0MB/s   00:00    
Fetching /home/kkeith/rnaseq_practice/data/fastqc/dac1_chr21_R2_fastqc.html to dac1_chr21_R2_fastqc.html
/home/kkeith/rnaseq_practice/data/fastqc/dac1_chr21_R2_fastqc.html         100%  238KB  42.4MB/s   00:00    
Fetching /home/kkeith/rnaseq_practice/data/fastqc/dac2_chr21_R1_fastqc.html to dac2_chr21_R1_fastqc.html
/home/kkeith/rnaseq_practice/data/fastqc/dac2_chr21_R1_fastqc.html         100%  234KB  42.3MB/s   00:00    
Fetching /home/kkeith/rnaseq_practice/data/fastqc/dac2_chr21_R2_fastqc.html to dac2_chr21_R2_fastqc.html
/home/kkeith/rnaseq_practice/data/fastqc/dac2_chr21_R2_fastqc.html         100%  232KB  46.3MB/s   00:00    
Fetching /home/kkeith/rnaseq_practice/data/fastqc/dac3_chr21_R1_fastqc.html to dac3_chr21_R1_fastqc.html
/home/kkeith/rnaseq_practice/data/fastqc/dac3_chr21_R1_fastqc.html         100%  237KB  51.6MB/s   00:00    
Fetching /home/kkeith/rnaseq_practice/data/fastqc/dac3_chr21_R2_fastqc.html to dac3_chr21_R2_fastqc.html
/home/kkeith/rnaseq_practice/data/fastqc/dac3_chr21_R2_fastqc.html         100%  234KB  53.7MB/s   00:00    
Fetching /home/kkeith/rnaseq_practice/data/fastqc/siC1_chr21_R1_fastqc.html to siC1_chr21_R1_fastqc.html
/home/kkeith/rnaseq_practice/data/fastqc/siC1_chr21_R1_fastqc.html         100%  243KB  53.1MB/s   00:00    
Fetching /home/kkeith/rnaseq_practice/data/fastqc/siC1_chr21_R2_fastqc.html to siC1_chr21_R2_fastqc.html
/home/kkeith/rnaseq_practice/data/fastqc/siC1_chr21_R2_fastqc.html         100%  234KB  55.8MB/s   00:00    
Fetching /home/kkeith/rnaseq_practice/data/fastqc/siC2_chr21_R1_fastqc.html to siC2_chr21_R1_fastqc.html
/home/kkeith/rnaseq_practice/data/fastqc/siC2_chr21_R1_fastqc.html         100%  240KB  56.6MB/s   00:00    
Fetching /home/kkeith/rnaseq_practice/data/fastqc/siC2_chr21_R2_fastqc.html to siC2_chr21_R2_fastqc.html
/home/kkeith/rnaseq_practice/data/fastqc/siC2_chr21_R2_fastqc.html         100%  233KB  59.4MB/s   00:00    
Fetching /home/kkeith/rnaseq_practice/data/fastqc/siC3_chr21_R1_fastqc.html to siC3_chr21_R1_fastqc.html
/home/kkeith/rnaseq_practice/data/fastqc/siC3_chr21_R1_fastqc.html         100%  236KB  60.9MB/s   00:00    
Fetching /home/kkeith/rnaseq_practice/data/fastqc/siC3_chr21_R2_fastqc.html to siC3_chr21_R2_fastqc.html
/home/kkeith/rnaseq_practice/data/fastqc/siC3_chr21_R2_fastqc.html         100%  233KB  63.4MB/s   00:00

Uploading

To upload to the server from your local (personal) computer, use the command put.

### upload files to the server
### Generally, to run commands to see stuff on your local (personal computer), put an l in front fo the command
# check your local (personal computer) location 
sftp> lpwd
Local working directory: /Users/kelsey/Documents/2020_bioinformatics_research_experience/rnaseq-demo
# list the files  on your local (personal computer) location; for example I can see the FastQC html reports I just downloaded
sftp> llls
README.md			dac3_chr21_R1_fastqc.html	siC2_chr21_R2_fastqc.html
dac1_chr21_R1_fastqc.html	dac3_chr21_R2_fastqc.html	siC3_chr21_R1_fastqc.html
dac1_chr21_R2_fastqc.html	siC1_chr21_R1_fastqc.html	siC3_chr21_R2_fastqc.html
dac2_chr21_R1_fastqc.html	siC1_chr21_R2_fastqc.html
dac2_chr21_R2_fastqc.html	siC2_chr21_R1_fastqc.html
# If I want to upload my README file with my documentation for the project to the main rnaseq_practice directory, use put and specify the file path
sftp> put README.md ../../
# show that it's where you expect
sftp> cd ../../
sftp> pwd
Remote working directory: /home/kkeith/rnaseq_practice
sftp> ls
README.md   analysis    data