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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 1 | + | more ~/DSCI512_RNAseq/PROJ03GomezOrte1/metadata_gomezOrte.txt |
| - | SRR3567552_1.fastq SRR3567552_2.fastq sample02 CK45-2 untreated 45min 2 | + | 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 1 | + | 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 2 | + | 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 1 | + | SRR5832185_1.fastq SRR5832185_2.fastq EG04 04_Ecoli_20_1 Ecoli 20 1 |
| - | SRR3567676_1.fastq SRR3567676_2.fastq sample10 CK200-2 untreated 200min 2 | + | 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 1 | + | 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 2 | ||
| + | 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 1 | ||
| + | SRR5832192_1.fastq SRR5832192_2.fastq EG11 11_Bsubtilis_15_2 Bsubtilis 15 2 | ||
| + | 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 1 | ||
| + | SRR5832195_1.fastq SRR5832195_2.fastq EG14 14_Bsubtilis_20_2 Bsubtilis 20 2 | ||
| + | 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 1 | ||
| + | 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> | ||
| Line 28: | Line 39: | ||
| **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> | ||
| Line 56: | Line 54: | ||
| ===== 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**\\ | ||
| Line 76: | Line 74: | ||
| # 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
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