UploadLargeData: Difference between revisions

From Cheaha
Jump to navigation Jump to search
No edit summary
(removed page. Left links to other related pages. It was redundent.)
 
(One intermediate revision by one other user not shown)
Line 1: Line 1:
= Load and Link approach =
= Page removed =


 
Please see [[Galaxy_File_Uploads]] for an overview and [[Galaxy_Data_Import]] for large datasets.
== transfer and uncompress (slow) ==
# login to cheaha.uabgrid.uab.edu (linux),
# create directory for this data set in your scratch dir
## mkdir /lustre/scratch/''user''/proj1
## make sure that directory is readable by galaxy user
### Chmod og+x /lustre/scratch/''user''
### Chmod og+x /lustre/scratch/''user''/proj1
# transfer the files with SCP
## scp *.fastq.gz ''user''@cheaha.uabgrid.uab.edu:/lustre/scratch/''user''/proj1
## I used "Secure Shell Client" for windows, available at [http://www.uab.edu/it/software/displaytitle.php?ItemID=34 UABIT]
## open source client is [http://www.chiark.greenend.org.uk/~sgtatham/putty/ PuTTY]
# '''UNCOMPRESS fastq.gz files!!'''
## cd /lustre/scratch/''user''/proj1
### gzip -d ''filename''
### !!WARNING: the following parallel decompress stesp fail for docs over 8G uncompressed!!
### find `pwd` -name "*.gz" -exec ksh -c 'qrsh "gzip -d \{}" &' \;
### ls -1 *.gz | xargs -L 1 -i_f_ ksh -c 'qrsh -cwd gzip -d _f_ &' \;
# make sure the files are readable by galaxy
## if you're in galaxy-admin UNIX group you can do
### chgrp galaxy-admin *.fastq
### chmod g+r *.fastq
## if you're not, then you have to make it readable to the world (o=other)
###  chmod o+r /lustre/scratch/''user''/proj1/*
 
== link into galaxy dataset (fast) ==
# get Admin privileges on galaxy
## either get Shantanu to make you admin in Galaxy
## or grab someone who is (John, Curtis)
# In Galaxy GUI:
## admin > Manage Data Libraries > create new library
### add Datasets
#### Upload option: Upload files from system path
##### Get a list of absolute path names using one of the following
###### cd /lustre/scratch/''user''/proj1 THEN RUN find `pwd` -name "*.fastq"
###### find /lustre/scratch/''user''/proj1 -name "*.fastq"
##### paste list of absolute path names into URL/Text box in Web Admin GUI
#### Change "Copy data into Galaxy?" to "Link to files without copying into Galaxy"
#### Put something mnemonic in Message box.
 
== link data into a history (fast) ==
 
I could then select the datasets and, at bottom of page "For selected datasets: <Import to histories>" and get them into a history so I can compute on them.

Latest revision as of 19:37, 7 March 2013

Page removed

Please see Galaxy_File_Uploads for an overview and Galaxy_Data_Import for large datasets.