Tag Archives: curl

Sequencing Data – C.gigas Larvae OA

Our sequencing data (Illumina HiSeq2500, 100SE) for this project has completed by Univ. of Oregon Genomics Core Facility (order number 2212).

Samples sequenced/pooled for this run:

Sample Treatment Barcode
400ppm 400ppm GCCAAT
1000ppm 1000ppm CTTGTA

 

All code listed below was run on OS X 10.9.5

Ran a bash script called “download.sh” to download all the files. The script contents were:

#!/bin/bash
curl -O http://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_001.fastq.gz
curl -O http://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_002.fastq.gz
curl -O http://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_003.fastq.gz
curl -O http://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_004.fastq.gz
curl -O http://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_005.fastq.gz
curl -O http://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_006.fastq.gz
curl -O http://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_007.fastq.gz
curl -O http://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_008.fastq.gz
curl -O http://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_009.fastq.gz
curl -O http://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_010.fastq.gz
curl -O http://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_011.fastq.gz
curl -O http://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_012.fastq.gz

 

Downloaded all 12 fastq.gz files to Owl/web/nightingales/C_gigas

Renamed all files by removing the beginning of each file name (2112?fileName=) and replacing that with 2212_:

$for file in 2212*lane2_NoIndex_L002_R1_0*; do mv "$file" "${file/#2212?fileName=/2212_}"; done

 

Created a directory readme.md (markdown) file to list & describe directory contents: readme.md

$ls *.gz >> readme.md

Note: In order for the readme file to appear in the web directory listing, the file cannot be all upper-case.

 

Create MD5 checksums for each the files: checkums.md5

$md5 2212* >> checksums.md5

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Sequencing Data – LSU C.virginica MBD BS-Seq

Our sequencing data (Illumina HiSeq2500, 100SE) for this project has completed by Univ. of Oregon Genomics Core Facility (order number 2112).

Samples sequenced/pooled for this run:

Sample Treatment Barcode
HB2 25,000ppm oil ATCACG
HB16 25,000ppm oil TTAGGC
HB30 25,000ppm oil TGACCA
NB3 No oil ACAGTG
NB6 No oil GCCAAT
NB11 No oil CAGATC

All code listed below was run on OS X 10.9.5

Downloaded all 15 fastq.gz files to Owl/web/nightingales/C_virginica:

$curl -O http://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_001.fastq.gz
$curl -O http://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_002.fastq.gz
$curl -O http://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_003.fastq.gz
$curl -O http://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_004.fastq.gz
$curl -O http://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_005.fastq.gz
$curl -O http://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_006.fastq.gz
$curl -O http://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_007.fastq.gz
$curl -O http://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_008.fastq.gz
$curl -O http://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_009.fastq.gz
$curl -O http://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_010.fastq.gz
$curl -O http://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_011.fastq.gz
$curl -O http://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_012.fastq.gz
$curl -O http://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_013.fastq.gz
$curl -O http://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_014.fastq.gz
$curl -O http://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_015.fastq.gz

 

Renamed all files by removing the beginning of each file name (2112?fileName=) and replacing that with 2112_:

$for file in 2112*lane1_NoIndex_L001_R1_0*; do mv "$file" "${file/#2112?fileName=/2112_}"; done

 

Created a directory readme.md (markdown) file to list & describe directory contents: readme.md

$ls *.gz >> readme.md

Note: In order for the readme file to appear in the web directory listing, the file cannot be all upper-case.

 

Created MD5 checksums for each fastq.gz file: checksums.md5

$md5 *.gz >> checksums.md5

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