User: yliu41

gravatar for yliu41
yliu4150
Reputation:
50
Status:
Trusted
Location:
Last seen:
1 month, 1 week ago
Joined:
8 months, 1 week ago
Email:
y*****@wustl.edu

Posts by yliu41

<prev • 12 results • page 1 of 2 • next >
0
votes
1
answer
62
views
1
answer
Tests on a tool with an input of type data_collection
... Hello folks, My Tool#1 is using a data_collection type created by Tool#2 as an input parameter. Below is how the collection is created in Tool#2: Now, I want to write a test case for my Tool#1. But I am not sure how to specify individua ...
collection data_collection development planemo written 6 weeks ago by yliu4150 • updated 6 weeks ago by Jennifer Hillman Jackson23k
0
votes
1
answer
210
views
1
answer
How to free up space on Galaxy server (purge history doesn't delete files)
... Hello, We are about to run out of space on our Galaxy instance. I purged some histories in order to free up some space. However, no space is freed. No files are deleted after I purge the histories. Do I need to manually delete all the files? Thank you! Best, Yating ...
galaxy written 4 months ago by yliu4150 • updated 4 months ago by Martin Čech ♦♦ 4.2k
2
votes
1
answer
198
views
1
answers
Comment: C: View bam files on UCSC genome browser (Galaxy display application)
... Thank you Jen! It is very helpful! I have another question: my database is mm10, but it is not in Galaxy dataset's metadata (database/build). I found mm9 in it. How can I add mm10 to Galaxy? Thanks a lot. ...
written 4 months ago by yliu4150
4
votes
1
answer
198
views
1
answer
View bam files on UCSC genome browser (Galaxy display application)
... Hello folks, I want to view BAM files on UCSC genome browser. I got my BAM files from HISAT2. But I don't see a link for viewing them on UCSC genome browser. I saw there is bam.xml in /display_applications/ucsc/. And in datatypes_conf.xml.sample, it shows bam can display on ucsc: ...
bam written 4 months ago by yliu4150 • updated 4 months ago by Jennifer Hillman Jackson23k
1
vote
2
answers
217
views
2
answers
Comment: C: Data managers tool: the content of data table disappear after restart Galaxy
... Thank you for the information! I found why it happened. After I searched for all *loc file, I found there was no loc file in data_manager tool directory. I deleted and reinstalled the data manager tool. It created a loc file in its directory and everything works. I used testtoolshed to test the too ...
written 7 months ago by yliu4150
0
votes
2
answers
217
views
2
answers
Comment: C: Data managers tool: the content of data table disappear after restart Galaxy
... I tested the tool (https://testtoolshed.g2.bx.psu.edu/repository?repository_id=a09497a087b272fe&changeset_revision=c5f8cd66db69) in a Galaxy virtual machine instance. The loc file is only used for one tool (https://toolshed.g2.bx.psu.edu/repository?repository_id=05cfe76518348625&changeset_re ...
written 7 months ago by yliu4150
3
votes
2
answers
217
views
2
answers
Data managers tool: the content of data table disappear after restart Galaxy
... Hi there, I am developing a data managers tool to add trained data. The tool works and can create a entry to the data table every time it runs. However, after I restart Galaxy instance, the entries in the data table are gone. I am wondering if we need to fetch the data again after restart the sys ...
galaxy written 7 months ago by yliu4150 • updated 7 months ago by y.hoogstrate450
1
vote
1
answer
137
views
1
answers
Answer: A: Data managers tool generates path has extra slash
... I found a way to get around this issue by add abspath ...
written 7 months ago by yliu4150
1
vote
1
answer
137
views
1
answer
Data managers tool generates path has extra slash
... Hi there, I am developing a data managers tool to install training data for GlimmerHMM. But now the tool generates file path has extra slash: Data Manager: glimmer_hmm_trained_dir value name path human human tool-data/human//home/galaxy/galaxy/database/jobs_directory/000/230/dataset ...
galaxy written 7 months ago by yliu4150
0
votes
2
answers
283
views
2
answers
Comment: C: How can I get the ip address of a running Galaxy instance
... It worked! Thank you very much! Best, Yating ...
written 8 months ago by yliu4150

Latest awards to yliu41

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 101 users visited in the last hour