User: 18Kbeyond

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18Kbeyond20
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New York
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y*****@columbia.edu

Posts by 18Kbeyond

<prev • 26 results • page 2 of 3 • next >
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Can I keep "on data xx" when including label in output
... Hi. I feel it's very helpful to have "on data xx" in the output name, as the default output name displays. e.g. filer_file_on_data_1 Is there a way I can have "on data xx" when I include "label" option in output like below? mutationType is an input parameter which is a select list. < data nam ...
output label written 3 months ago by 18Kbeyond20
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Is it possible to auto-detect the database/genome of the input file?
... Hi. I am writing xml scripts that will ask the users to pick a reference genome (e.g. hg19, mm10, etc. ). Is there a way that it can auto-detect that, as the database of the input file is known? Or the default can auto-change to the same database of the input file ...
database genome auto-detect written 3 months ago by 18Kbeyond20 • updated 3 months ago by Jennifer Hillman Jackson23k
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please help! accidentally removed some files
... Sorry for this kind of question but I accidentally removed these with rm -rf s*: setup.cfg, scripts folder and static folder Is there a place I can find them and restore them? ...
files galaxy distribution admin written 3 months ago by 18Kbeyond20 • updated 3 months ago by Jennifer Hillman Jackson23k
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Is && needed in xml for seperating lines?
... Hi. I see an example here https://docs.galaxyproject.org/en/latest/dev/schema.html that **&&** is used to separate two lines: mkdir -p output_dir **&&** python $__tool_directory__/extract_genomic_dna.py However, when I used **&&** in my xml, it doesn't work - it is not sho ...
&amp;&amp; written 3 months ago by 18Kbeyond20 • updated 3 months ago by Devon Ryan1.9k
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Answer: A: How do I add my own reference genome for mapping RNA-seq data
... First, index samples and save them in a path. say home/galaxy/galaxy_data/genomes/ Then, make changes like below in tool-data/bwa_mem_index.loc according to tool-data/bwa_mem_index.loc.sample hg19bwa hg19 hg19 Canonical /home/galaxy/galaxy_data/genomes/hg19/bwa/hg19.fa mm10bwa mm10 mm10 Canonical ...
written 3 months ago by 18Kbeyond20
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Comment: C: How to configure genome in "Map with BWA" (existing tool) after adding it to my
... However, when I execute the job, it generates the following error: Traceback (most recent call last): File "/data/galaxy/lib/galaxy/jobs/runners/local.py", line 130, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/data/galaxy/lib/galaxy/jobs/__init__.py", line 1266, in finish ...
written 3 months ago by 18Kbeyond20
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Answer: A: How to add a new data type -- "sai"
... I did these and it works In binary.py file, add: class Sai( Binary ): """Class describing a Sai file""" file_ext = "sai" In registry.py file, add: 'sai' : binary.Sai(), ...
written 3 months ago by 18Kbeyond20
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How to add a new data type -- "sai"
... Hi. I need to add a new data type "sai" as an output from bwa aln. I am reading https://galaxyproject.org/admin/datatypes/adding-datatypes/ but I am not sure what to do for step 3. As I don't need to upload sai files for now I am skipping step 2. I have done step 1 -- I added the line below to th ...
data type sai written 3 months ago by 18Kbeyond20
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Comment: C: How to configure genome in "Map with BWA" (existing tool) after adding it to my
... Thank you. Instead of installing data manager from the tool shed, I made my own genome and index and make changes in tool-data/bwa_mem_index.loc hg19bwa hg19 hg19 Canonical /home/galaxy/galaxy_data/genomes/hg19/bwa/hg19.fa mm10bwa mm10 mm10 Canonical /home/galaxy/galaxy_data/genomes/mm10/ ...
written 3 months ago by 18Kbeyond20
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How to configure genome in "Map with BWA" (existing tool) after adding it to my local section
... Hi. I have added the lines below to the section I made in config/tool_conf.xml file and "Map with BWA" is showing up on galaxy interface when I execute run.sh. However, I can't pick a genome in the "Using reference genome" box. What modification should I make in shed_tools/toolshed.g2.bx.psu.edu/re ...
index local galaxy data-managers genome written 3 months ago by 18Kbeyond20 • updated 3 months ago by Jennifer Hillman Jackson23k

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