problem with downloading files
1
1
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4.5 years ago
elisheva ▴ 110

Hello everyone!
I have a problem with downloading files from ensembl.
I am trying to download some files using rsync command.
I have a text file of all the paths for all the file.
The problem is that I can't extract them.
Here is my shell script:

#!/bin/bash
while read line
do
echo $line
rsync -av $line 
done < path.txt

while path.txt is this txt file:

rsync://ftp.ensembl.org/ensembl/pub/release-89/fasta/ailuropoda_melanoleuca/cdna/Ailuropoda_melanoleuca.ailMel1.cdna.all.fa.gz ./
rsync://ftp.ensembl.org/ensembl/pub/release-89/fasta/anas_platyrhynchos/cdna/Anas_platyrhynchos.BGI_duck_1.0.cdna.all.fa.gz ./

of course there are much more paths.

I did all this according to ensemble instructions: http://www.ensembl.org/info/data/ftp/rsync.html
For one path it works quite well....
The problem is for more than one file...
Using tar or gunzip did not help.
Can someone solve this problem?
Thanks!!

rsync ensembl • 1.7k views
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0
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Your example script works fine for me, is there an error message your are getting?

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0
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I couldn't extract the files. But I changed it, so now the text file looks like this: rsync -av ..... path. for each line. and it worked fine.

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2
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4.5 years ago
Emily 23k

Your ftp links should begin:

rsync://ftp.ensembl.org/pub/release-89/fasta/
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1
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It doesn't work - I get an error when I run it...
on http://www.ensembl.org/info/data/ftp/rsync.html
It says to add the ensembl/

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