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Helena Rasche
@hexylena:matrix.org
[m]
huh
Ariel Erijman
@aerijman
yes
Simon Bray
@simonbray:matrix.org
[m]
why not just use show_history?
Ariel Erijman
@aerijman
I go like this:
# 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
Simon Bray
@simonbray:matrix.org
[m]
what about using parsec histories show_history ${id} --contents instead?
Ariel Erijman
@aerijman
I will try now. Last time I used it it worked fine though
(galaxy_histories) aerijman@seq-
himem02:/data$ 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'
Simon Bray
@simonbray:matrix.org
[m]
it seems argparse creates a tuple for types and bioblend doesn't like that
maybe you can get round it with parsec histories show_history ${id} --contents --types dataset dataset_collection
Helena Rasche
@hexylena:matrix.org
[m]
ok, yikes, that's something we'll need to work around in parsec.
parsec histories show_history ${id} --contents should be working
I thought I used that the other day
Simon Bray
@simonbray:matrix.org
[m]
possibly you and @aerijman have different bioblend versions
Helena Rasche
@hexylena:matrix.org
[m] 
$ 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"
    }
]
Simon Bray
@simonbray:matrix.org
[m]
try updating to a more recent bioblend @aerijman ?
simonbray
@simonbray:matrix.org
[m]
Cool, thanks for that
Wesley Jones
@joneswac:matrix.org
[m]

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().

Dannon
@dannon
Might be a bug, I can try to look in a few. That URL may or may not take the galaxy base url into account.
1 reply
Wesley Jones
@joneswac:matrix.org
[m]
Thanks. I suspect you're right. When I use a SSH tunnel to connect to the localhost port that the app is running on everything loads correctly, and for that it doesn't seem to care about the mountpoint.
Ariel Erijman
@aerijman
Sorry, I, forcibly, went offline. I updated bioblend from 0.12.0 to 0.15.0 but I am still getting the same error. I am wondering... I haven't changed anything in my conda environment nor my scripts... It might be something on the galaxy end that could affect parsec?
4 replies
galaxybot
@galaxybot

[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…

galaxybot
@galaxybot

[unknown]
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…

zekunyang
@zekunyang
Excuse me, how to set the location of the upload file and the output file of the task in galaxy
Qiang Gu
@qiagu
@zekunyang try config/galaxy.yml.
Anne Fouilloux
@annefou

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:

  • how to test locally (apart from uploading a file and checking "manually").
  • I can't find any info related to testing new datatypes so I guess it is obvious but unfortunately not for me...
    Can anyone point me to where to start?
bgruening
@bgruening:matrix.org
[m]
@annefou: there is a script called ./run_tests.sh that you can probably use
but I think you are missing the example file in your PR
ColineRoyaux
@ColineRoyaux

So Coline, the error message is requests.exceptions.HTTPError: 404 Client Error: Not Found for url: https://wheels.galaxyproject.org/simple/adal/

Hi everyone ! I'm still getting the same issue with planemo, it seems like planemo searches for adal with the wrong URL

I also tried to install planemo on an other computer and I got the same error...
Any idea ?
viktoriaas
@viktoriaas

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

FumiSuomi
@FumiSuomi
Hi, I'm trying to extract genomic DNA from a bed file I generated from recently updated Biomart/Ensembl GRCm39. Error code starting with "Unable to fetch the sequence ---". GRCm39/mm39 is used for database. I tried GRCm38 and it gives the same error. Any tips?
galaxybot
@galaxybot

[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…

stvlar
@stvlar
hello, do you have any recommendations for which platforms would be the best to deploy my own galaxy server? it will (hopefully) be used by a substantial amount of people but i'm hoping to find something with the smallest possible cost https://galaxyproject.org/use/
Abdalrhmanibrahim98
@Abdalrhmanibrahim98
Hello, I am trying to trim a FASTQ file (actually they're two; R1 and R2) using trimmomatic, but it keeps giving a red-coloured error that says "an error occurred with this dataset". does anyone know how can I overcome this error?
Cristóbal Gallardo
@gallardoalba
Hi @Abdalrhmanibrahim98, could you share your history with me?, I can have a look
Abdalrhmanibrahim98
@Abdalrhmanibrahim98
@gallardoalba You can access the history via: https://usegalaxy.org/u/abdalrhman.ibrahim/h/unnamed-history
The job is still in the queue as I purged the errored jobs and started it over again.
I am pretty sure this job will give the same error as well because I used the same parameters used when it gave me the errors.
Thanks for your help :)
I'm just wondering if something is wrong about my datasets or about the way I used trimmomatic
Cristóbal Gallardo
@gallardoalba
Nice, I'll check it
Abdalrhmanibrahim98
@Abdalrhmanibrahim98
Okay thanks
Cristóbal Gallardo
@gallardoalba
Hi @abdulrahmanazab , the problem is that Trimmomatic cannot find the Phred quality encoding. I opened an issue in order to fix it fls-bioinformatics-core/galaxy-tools#79. I suggest you use a different tool until the problem is solved (e.g. Cutadapt or fastp). Regards
galaxybot
@galaxybot
[unknown]
Request for metaviralSPAdes [usegalaxy.org.au support] tool-install, tool-dev, toolshed, metagenomics
Hi all, I would like to request adding the tool metaviralSPAdes to the Galaxy au toolshed. metaviralSPAdes is a variant of the current metaS…
Abdalrhmanibrahim98
@Abdalrhmanibrahim98
Thank you so much, @gallardoalba
galaxybot
@galaxybot

[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…

galaxybot
@galaxybot
[unknown]
BioTradis empty counts output [usegalaxy.org support] error
I have a sequenced Transposon-insertion mutant library and I wish to find the number of unique mutants/ insertions in the library. I used Bi…
Michael
@mchlou
hello, just wanted to ask, is there a way to get a consensus sequence from sequences mapped with reference sequences using BWA Mem? i have a transcriptome sequence and would like to extract all possible viral sequences from my data. I mapped all contigs in NCBI viral database. thank you
galaxybot
@galaxybot

[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…

galaxybot
@galaxybot

[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…

Ameirika
@Ameirika_twitter
Hi all. I would like to ask about macs software. I am just wondering what the different between the peak calling using macs2 and Deduct noise by comparing two signal tracks in bedGraph using macs?. How deduct noise by comparing two signal tracts is work? and does this deduct noise is considered as peak calling?