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pvanheus
@pvanheus
@jennaj they could something like the from-user-directory library import? https://galaxyproject.org/data-libraries/#from-user-folder
(and then use "link files instead of copying" if the user-folder stuff is going to be permanent)
Tomas
@TKlingstrom
I also got a library problem
Running a docker with the command:
docker run -p 8084:80 --name Ebba4 -v galaxy-test2:/export/ -e "GALAXY_CONFIG_BRAND=Friday" -e "GALAXY_CONFIG_USER_LIBRARY_IMPORT_DIR=/export/userlib" -e "GALAXY_CONFIG_USER_LIBRARY_IMPORT_DIR_AUTO_CREATION=true" bgruening/galaxy-stable
(absolut path due to debugging after previous chat with @martenson and Björn for debug)
The folder shows up perfectly as expected and are created when new users signs up.
But the library folders are not accessible through the GUI
Martin Cech
@martenson
@jennaj @pvanheus I suspect metadata is what slows them down
Jennifer Hillman-Jackson
@jennaj
@pvanheus I wasn't sure if that worked anymore. There are also the new collection uploader methods introduced in 18.05 ... but I don't think any of those keep galaxy from eventually ... well, what martin just said :)
pvanheus
@pvanheus
@martenson ah yes, it will scan that massive file. also if it is imported as fastq instead of fastq.gz it will be unpacked.
Jennifer Hillman-Jackson
@jennaj
right, the unpacking takes time. there is some chat about that, e.g. not unpacking if the file is .gz
pvanheus
@pvanheus
yes, but you need to explicitely select to store as gz - and I'm never sure which is the better option - of course, for disk space, compressed is good - but it will be unpacked to analyse anyway..
Jennifer Hillman-Jackson
@jennaj
I'm all for that - it isn't obvious that one should set the datatype during upload to a gz format to preserve that and not unpack
true
not all legacy tools accept gz .. likely only a problem on some public sites like .org
pvanheus
@pvanheus
but gz or not, that metadata scanning is going to take time. and I don't think that can be disabled.
Jennifer Hillman-Jackson
@jennaj
I don't think so either but suspect that someone, somewhere has hacked their Galaxy to not do it .. and take on all the risks involved with that (directly assigning metadata without some sanity checks)
pvanheus
@pvanheus
@jennaj add "fastq-withfakeseqcount" datatype with no sequence counting (because the slow part is this: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/sequence.py#L553) :)
Jennifer Hillman-Jackson
@jennaj
funny and probably useful for local servers with a lot of production throughput. the data probably goes through some type of validator/firewall even before going into Galaxy anyway
but don't change the public sites! please :)
since we started doing more sniffing, errors rooted all the way back to a problematic upload have reduced significantly, so it helps
pvanheus
@pvanheus
the data manager I'm working on moves files to tool-data/seq/whole/long/path/to/dataset - in the data_manager_conf.xml can you use functions like os.path.basename in e.g. the target specification of a move?
Jennifer Hillman-Jackson
@jennaj
I don't know -- someone else will have to comment -- maybe @blankenberg ?
pvanheus
@pvanheus
seems you can't... or rather there probably is some way I don't know about...
Jennifer Hillman-Jackson
@jennaj
I remember hard links being important in other areas of DMs before, so might be necessary. Let's see what dan says :)
pvanheus
@pvanheus
Thanks @jennaj with the help of reading the source and some testing I figure out what is going on... I will update the docs to be more explicit
modejurtysuneeta
@modejurtysuneeta
Hi
Planning the project Comparing DNA sequences of different species
Please give inputs on the databases and tools I can use to best do the project
pvanheus
@pvanheus
@modejurtysuneeta are you comparing assembled genomes? then lastz could work. What type of species are these?
and what scientific question are you investigating?
Anup Kumar
@anuprulez
Nicola Soranzo
@nsoranzo
Part of it is outdated unfortunately
Tomas
@TKlingstrom
What log should I look into to see if I got an access denied for my data library? I got a Library_import_dir configured and Galaxy autocreates the user folders as expected but I cannot see any data libraries when logging in as a user.
My best bet is that it is a conflict caused by permissions but I am not sure where it is logged. I am using the Grüning dockers btw (in case you want to try it: docker run -p 8083:80 --name Ebba3 -v /export/ -e "GALAXY_CONFIG_BRAND=Sunday" -e "GALAXY_CONFIG_USER_LIBRARY_IMPORT_DIR=/export/userlib" -e "GALAXY_CONFIG_USER_LIBRARY_IMPORT_DIR_AUTO_CREATION=true" -e "GALAXY_LOGGING=full" bgruening/galaxy-stable)
modejurtysuneeta
@modejurtysuneeta
I downloaded a file
i downloaded a vcf.gz file from 1000genome into my linux terminal.
how to decompress it?
Should I directly give unzip file command?
or shouldni give zip file command?
I mean should I give zip file command?
M new to programming
aditya235
@aditya235
HELLO
I have recently installed local galaxy but unable to install tools
is this a problom from galaxy server
?
selten
@selten
What do the logs say?
Tomas
@TKlingstrom

I decided to test the data library suggestion that I could mount the FTP server as my data library. My files shows up in the FTP folder but not in the data libraries list.

Do you perhaps have an idea on this @martenson based on the permission discussion on Friday?

Command I ran:
docker run -p8082:80 --name Ebba2 -v monlibftp:/export/ -e "GALAXY_CONFIG_BRAND=Sunday" -e "GALAXY_CONFIG_USER_LIBRARY_IMPORT_DIR=/export/ftp" -e "GALAXY_CONFIG_USER_LIBRARY_IMPORT_DIR_AUTO_CREATION=true" -e "GALAXY_LOGGING=full" bgruening/galaxy-stable

Tomas
@TKlingstrom
So I do not think its the permissions that are off. Am I perhaps missing something obvious? The only configurations I do is to set the ENV variables in the Docker runt command.