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wiki:automation [2018/11/29 09:24]
erin
wiki:automation [2019/12/04 22:47] (current)
erin
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 The key is to use the information in the ''​metadata''​ file to instruct a series of commands to loop over each field. The key is to use the information in the ''​metadata''​ file to instruct a series of commands to loop over each field.
  
-Let's take a look at the ''​metadata''​ file for our yeast demo project: ​+Let's take a look at the ''​metadata''​ file for our //C. elegans// ​demo project: ​
  
 <code bash> <code bash>
-SRR3567551_1.fastq SRR3567551_2.fastq sample01 CK45-1 untreated 45min +more ~/​DSCI512_RNAseq/​PROJ03GomezOrte1/​metadata_gomezOrte.txt 
-SRR3567552_1.fastq SRR3567552_2.fastq sample02 CK45-2 untreated 45min +SRR5832182_1.fastq ​     ​SRR5832182_2.fastq ​     ​EG01 ​   01_Ecoli_15_1 ​  ​Ecoli ​  ​15 ​     ​1 
-SRR3567554_1.fastq SRR3567554_2.fastq sample03 Ac45-1 aceticAcidTreated 45min +SRR5832183_1.fastq ​     SRR5832183_2.fastq ​     EG02    02_Ecoli_15_2 ​  ​Ecoli ​  ​15 ​     2 
-SRR3567555_1.fastq SRR3567555_2.fastq sample04 Ac45-2 aceticAcidTreated 45min +SRR5832184_1.fastq ​     SRR5832184_2.fastq ​     EG03    03_Ecoli_15_3 ​  ​Ecoli ​  ​15 ​     3 
-SRR3567674_1.fastq SRR3567674_2.fastq sample09 CK200-1 untreated 200min +SRR5832185_1.fastq ​     SRR5832185_2.fastq ​     EG04    04_Ecoli_20_1 ​  ​Ecoli ​  ​20 ​     ​
-SRR3567676_1.fastq SRR3567676_2.fastq sample10 CK200-2 untreated 200min +SRR5832186_1.fastq ​     ​SRR5832186_2.fastq ​     ​EG05 ​   05_Ecoli_20_2 ​  ​Ecoli ​  ​20 ​     ​2 
-SRR3567677_1.fastq SRR3567677_2.fastq sample11 Ac200-1 aceticAcidTreated 200min +SRR5832187_1.fastq ​     SRR5832187_2.fastq ​     EG06    06_Ecoli_20_3 ​  ​Ecoli ​  ​20 ​     3 
-SRR3567679_1.fastq SRR3567679_2.fastq sample12 Ac200-2 aceticAcidTreated 200min 2+SRR5832188_1.fastq ​     SRR5832188_2.fastq ​     EG07    07_Ecoli_25_2 ​  ​Ecoli ​  ​25 ​     1 
 +SRR5832189_1.fastq ​     SRR5832189_2.fastq ​     EG08    08_Ecoli_25_1 ​  ​Ecoli ​  ​25 ​     ​
 +SRR5832190_1.fastq ​     ​SRR5832190_2.fastq ​     ​EG09 ​   09_Ecoli_25_3 ​  ​Ecoli ​  ​25 ​     3 
 +SRR5832191_1.fastq ​     SRR5832191_2.fastq ​     EG10    10_Bsubtilis_15_1 ​      ​Bsubtilis ​      ​15 ​     ​
 +SRR5832192_1.fastq ​     ​SRR5832192_2.fastq ​     ​EG11 ​   11_Bsubtilis_15_2 ​      ​Bsubtilis ​      ​15 ​     ​
 +SRR5832193_1.fastq ​     ​SRR5832193_2.fastq ​     ​EG12 ​   12_Bsubtilis_15_3 ​      ​Bsubtilis ​      ​15 ​     3 
 +SRR5832194_1.fastq ​     SRR5832194_2.fastq ​     EG13    13_Bsubtilis_20_1 ​      ​Bsubtilis ​      ​20 ​     ​
 +SRR5832195_1.fastq ​     ​SRR5832195_2.fastq ​     ​EG14 ​   14_Bsubtilis_20_2 ​      ​Bsubtilis ​      ​20 ​     ​
 +SRR5832196_1.fastq ​     ​SRR5832196_2.fastq ​     ​EG15 ​   15_Bsubtilis_20_3 ​      ​Bsubtilis ​      ​20 ​     3 
 +SRR5832197_1.fastq ​     SRR5832197_2.fastq ​     EG16    16_Bsubtilis_25_1 ​      ​Bsubtilis ​      ​25 ​     ​
 +SRR5832198_1.fastq ​     ​SRR5832198_2.fastq ​     ​EG17 ​   17_Bsubtilis_25_2 ​      ​Bsubtilis ​      ​25 ​     ​2 
 +SRR5832199_1.fastq ​     SRR5832199_2.fastq ​     EG18    18_Bsubtilis_25_3 ​      ​Bsubtilis ​      ​25 ​     3
 </​code>​ </​code>​
  
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 **Make a new project directory:​** **Make a new project directory:​**
-  ​ 
-<code bash> 
-# Log into summit 
-$ ssh -l <​eID>​@colostate.edu login.rc.colorado.edu 
- 
-# switch to scompile 
-$ ssh scompile 
- 
-#If you want to, make your alias to scheck here 
-$ alias scheck='​squeue -u $USER' 
-</​code>​ 
- 
- 
-**Navigate to the space where you want to put your directory.** I'm putting mine in ''/​scratch/​summit/<​eID>​@colostate.edu/​DSCI512_RNAseq''​ 
  
 **Make a new directory & navigate into it:** **Make a new directory & navigate into it:**
  
 <code bash> <code bash>
-$ mkdir PROJ06_yeastDemo2 +$ pwd # You should be in DSCI512_RNAseq 
-$ cd PROJ06_yeastDemo2+$ mkdir PROJ04_GomezOrte2 
 +$ cd PROJ04_GomezOrte2
 </​code>​ </​code>​
  
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 ===== Create a soft link to the input data ===== ===== Create a soft link to the input data =====
  
-OK, we just started a new project. And we want to use the same input data as we used in the project ''​PROJ04_yeastDemo''​. One option would be to copy and paste the input files from that project over to this one. That would work, but it would be inefficient space-wise. ​+OK, we just started a new project. And we want to use the same input data as we used in the project ''​PROJ03_GomezOrte1''​. One option would be to copy and paste the input files from that project over to this one. That would work, but it would be inefficient space-wise. ​
  
-A better option would be to **point** the ''​PROJ06_yeastDemo2/​01_input''​ directory **to** the ''​PROJ04_yeastDemo/​01_input''​ directory. We can do this using **soft links**, also known as a **symbolic link**, also known as a **short cut**.+A better option would be to **point** the ''​PROJ04_GomezOrte2/​01_input''​ directory **to** the ''​PROJ03_GomezOrte1/​01_input''​ directory. We can do this using **soft links**, also known as a **symbolic link**, also known as a **short cut**.
  
 **Soft link usage**\\ **Soft link usage**\\
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 # create the softlink: # create the softlink:
-$ ln -s ../PROJ04_yeastDemo/01_input .+$ ln -s ../PROJ03_GomezOrte1/01_input .
  
 # check what you got using two different ls commands: # check what you got using two different ls commands:
wiki/automation.1543508695.txt.gz · Last modified: 2018/11/29 09:24 by erin