User: asmariyaz23

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asmariyaz2310
Reputation:
10
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New User
Location:
United States
Last seen:
1 week, 4 days ago
Joined:
3 years, 2 months ago
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a**********@gmail.com

Posts by asmariyaz23

<prev • 18 results • page 1 of 2 • next >
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Reserved variable for conda env in XML?
... Hello, Is there a reserved variable name like $__tool_directory__ for conda_prefix that can be accessed in the command section in an xml? A tool_script.sh is written when tool is executed which assigns the conda environment to a variable named $CONDA_DEFAULT_ENV. I would like to use that in the xml ...
xml conda reserved_variable written 13 days ago by asmariyaz2310 • updated 11 days ago by Bjoern Gruening5.1k
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Galaxy Url for Fasta and Bed index files
... Hello, What is an appropriate galaxy URL to use to obtain bed and fasta index files? I have tried below: myGalaxy.org:port/dataset/get_metadata_file?hda_id=[fasta_dataset_id]&metadata_name=fasta.fai {for fasta index} and  myGalaxy.org:port/dataset/get_metadata_file?hda_id=[bed_dataset_id]&am ...
index galaxy bed fasta written 2.7 years ago by asmariyaz2310
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Comment: C: Accessing bam file in history for visualization through Galaxy API
... I solved this issue by serving bam files through apache's modxsendfile (as suggested by carlfeberhard). IGV needs a Partial 206 content returned and Galaxy's server wasn't able to do it.  ...
written 2.9 years ago by asmariyaz2310
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Comment: C: Accessing bam file in history for visualization through Galaxy API
... I used the URL for the bam index file, but returns the following:  Request Range Not Satisfiable The Range requested is not available.  Invalid reference dataset id: get_metadata_file. I will soon write to the galaxy-dev list too! ...
written 3.0 years ago by asmariyaz2310
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Comment: C: Accessing bam file in history for visualization through Galaxy API
... Is there a way to access the .bai file associated with .bam file? The metadata has something of this sort: "meta_files": [{"file_type": "bam_index"}] when I access  http://kcodevel.broadinstitute.org:8088/galaxy/api/histories/[history id]/contents/[API ID]/display but have no clue how the file ...
written 3.0 years ago by asmariyaz2310
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Comment: C: Accessing bam file in history for visualization through Galaxy API
... Yes, I use a proxy so the URL is 'http://kcodevel.broadinstitute.org:8088/galaxy'. I have checked the error_log for apache and it looks like apache is trying to serve these bam files from htdocs area within apache folder. Here is the error log:  File does not exist: /seq/../kcodevel/apache/httpd/h ...
written 3.0 years ago by asmariyaz2310
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Comment: C: Accessing bam file in history for visualization through Galaxy API
... Upon your suggestion to add a "/" I did the following: 1)Extract API key and History ID of a newly loaded BAM file. 2) Include these 2 ids in the JSON object as below:  "CLL-HL_pilot.r1.fastq": { "DNA": "/galaxy/api/histories/[history id]/contents/[API ID]/display", "DNA_INDEX": "test.d ...
written 3.0 years ago by asmariyaz2310
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Accessing bam file in history for visualization through Galaxy API
... My goal is to use a JSON file (which is a product of a lab implemented pipeline ran on galaxy) for visualizing 2 BAM files (also produced by the pipeline) loaded in history. For this purpose I started out by loading the BAM and JSON individually in history and working my way from there (as I haven' ...
bam json galaxy visualization written 3.0 years ago by asmariyaz2310
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Comment: C: Adding new DataProvider for JSON
... Ok your solution worked like a charm!! Thanks... ...
written 3.0 years ago by asmariyaz2310
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Comment: C: Adding new DataProvider for JSON
... My goal is to retrieve a JSON dataset from history (which is an output of another pipeline) and feed this JSON dataset as a JSON object to the MutationInspector.js's. I will try to use the "dumps" method now.  ...
written 3.1 years ago by asmariyaz2310

Latest awards to asmariyaz23

Popular Question 2.6 years ago, created a question with more than 1,000 views. For Using a JSON object for visualization plugin
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Adding new DataProvider for JSON
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Serving galaxy with apache

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