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# each argument is a history name
for history_name in $@; do
# get id of history by name
id=$(parsec histories get_histories | jq -r --arg i "$history_name" 'map (select(.name == $i) | .id)' | tr -d ']["\n')
# use id to get data and parse that data
parsec histories show_matching_datasets ${id} | jq -r 'map (select(.deleted == false) | [.file_name, .name] | join ("\t")) | j
oin ("\n")' |\
while read file name; do
r=$(echo $name | sed -r 's/.*\.(.)\.fastq/\1/')
n=$(echo $name | sed -r s'/(.*)\..\.fastq/\1/')
echo "${n},${r},${file}"
done
parsec histories show_history ${id} --contents
instead?
himem02:/data$ parsec histories show_history ${id} --contents
Traceback (most recent call last):
File "/mnt/flash_scratch/aerijman/miniconda3/envs/galaxy_histories/lib/python3.6/site-packages/parsec/decorators.py", line 18, in custom_exception
return wrapped(*args, **kwargs)
File "/mnt/flash_scratch/aerijman/miniconda3/envs/galaxy_histories/lib/python3.6/site-packages/parsec/decorators.py", line 42, in dict_output
output = wrapped(*args, **kwargs)
File "/mnt/flash_scratch/aerijman/miniconda3/envs/galaxy_histories/lib/python3.6/site-packages/parsec/commands/histories/show_history.py", line 42, in cli
return ctx.gi.histories.show_history(history_id, contents=contents, deleted=deleted, visible=visible, details=details, types=types)
File "/mnt/flash_scratch/aerijman/miniconda3/envs/galaxy_histories/lib/python3.6/site-packages/bioblend/galaxy/histories/__init__.py", line 105, in show_history
params['types'] = types.join(",")
AttributeError: 'tuple' object has no attribute 'join'
'tuple' object has no attribute 'join'
parsec histories show_history ${id} --contents --types dataset dataset_collection
parsec histories show_history ${id} --contents
should be working
$ parsec --version
parsec, version 1.13.0
$ parsec histories show_history 2a1479b97d72f6fb --contents
[
{
"id": "11ac94870d0bb33a99393998ff667d7b",
"deleted": false,
"type": "file",
"hid": 1,
"type_id": "dataset-11ac94870d0bb33a99393998ff667d7b",
"purged": false,
"url": "/api/histories/2a1479b97d72f6fb/contents/11ac94870d0bb33a99393998ff667d7b",
"extension": "ipynb",
"create_time": "2021-04-01T10:43:50.159608",
"tags": [],
"state": "running",
"dataset_id": "11ac94870d0bb33a3dc9b3f66dfe1b39",
"history_content_type": "dataset",
"visible": true,
"name": "RStudio",
"update_time": "2021-04-01T20:23:07.670886",
"history_id": "2a1479b97d72f6fb"
}
]
Anyone familiar with Galaxy Reports running behind Apache (or NGINX) reverse proxy? I have the initial page HTML/CSS borders and menus displaying, but no content.
404 Not Found
The resource could not be found.
No route for /home/run_stats
I have mount point set in the config: mount: /reports=galaxy.webapps.reports.buildapp:uwsgi_app()
.
[unknown]
Workflow automation? [Uncategorized] workflow
Hello!
I have to fill parameters manually into my workflow which are mostly file names and sample names. I have to select from about 7 file…
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miRNA featureCounts [usegalaxy.eu support] mirna, featurecounts, transcriptomics
Hello everyone
I am working in Galaxy with miRNAs data.
I am trying to pass my reads mapped with Bowtie to counts with the featureCounts a…
Hi,
I am trying to add a new datatype (JPEG 2000) in Galaxy and I followed instructions at https://docs.galaxyproject.org/en/master/dev/data_types.html
The corresponding test is failing in the PR (galaxyproject/galaxy#11812) but
I don't understand:
Hi, does anyone know why such structure must exist in PVC when using galaxy on kubernetes? I don't see any point in this, deeper directories are all identical
[root@ntc1 pvc-b4a5a6bc-cb8b-4ecc-b1e3-1b61103d5b55]$ find . -iname "*jobs_directory*"
./jobs_directory
./tools/tools/jobs_directory
./tools/tools/tools/tools/jobs_directory
./tools/tools/tools/tools/tools/tools/jobs_directory
./tools/tools/tools/tools/tools/tools/tools/tools/jobs_directory
./tools/tools/tools/tools/tools/tools/tools/tools/tools/tools/jobs_directory
Each deployment template of job, workflow and web include the init container which runs these commands (from templates/_helpers.tpl)
{{/*
Creates the bash command for the init containers used to place files and change permissions in the galaxy pods
*/}}
{{- define "galaxy.init-container-commands" -}}
cp -anL /galaxy/server/config/integrated_tool_panel.xml /galaxy/server/config/mutable/integrated_tool_panel.xml;
cp -anL /galaxy/server/config/sanitize_allowlist.txt /galaxy/server/config/mutable/sanitize_allowlist.txt;
cp -anL /galaxy/server/config/data_manager_conf.xml.sample /galaxy/server/config/mutable/shed_data_manager_conf.xml;
cp -anL /galaxy/server/config/tool_data_table_conf.xml.sample /galaxy/server/config/mutable/shed_tool_data_table_conf.xml;
cp -aruL /galaxy/server/tool-data {{.Values.persistence.mountPath}}/;
cp -aruL /galaxy/server/tools {{.Values.persistence.mountPath}}/tools | true;
{{- end -}}
and the last true most probably causes this structure. But why??
Also, does anyone know what might cause this error?
[Errno 2] No such file or directory: SafeStringWrapper(str:__lt__class __sq__NoneType__sq____gt__,__lt__class __sq__NotImplementedType__sq____gt__,__lt__class __sq__bool__sq____gt__,__lt__class __sq__bytearray__sq____gt__,__lt__class __sq__ellipsis__sq___
It appeared out of nothing, everything was fine and then just stopped working
[unknown]
Extracting transcripts from whole-transcriptome libraries [Uncategorized] rna-seq, vcf-filter
Hi there,
I am having trouble finding a tool that will successfully extract specific transcripts from whole transcriptome libraries. The tr…
[unknown]
Store on HDD, run on SSD? [Uncategorized] admin
Hello!
Our server has only 1.5 tb ssd so it can store only about 4 runs of our workflow. And there is a plan to use it by multiple users, s…
[unknown]
Debugging a stuck workflow [Uncategorized] workflow
Hi there
I have a workflow invocation that seems to be stuck despite on some level being reported as running. This workflow takes two input…
[unknown]
Strandness option disappeared in Bowtie2 [usegalaxy.org support] rna-seq, bowtie2
Heyya,
I ran Bowtie2 today and I couldn’t find the strand-specificity option. Is there a new update? I doubt I missed it, it was under “Pai…