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Sailee
@psy_leee_twitter
I did look through the topics there, most of them say to make a local Galaxy server. I wanted to avoid that since I have already processed 30 fastq files on the usegalaxy.org server until the customProDB step. But I guess I will have to try the dual boot now. Thank you for your suggestion.
Nolan Woods
@innovate-invent
does windows 10 run docker?
Sailee
@psy_leee_twitter
I have not looked into that yet, maybe that can work. Thanks
galaxybot
@galaxybot

[unknown]
Missing tools and running local Galaxy instance on Windows 10 [usegalaxy.org support]
Hello,

I have been trying to create a protein database from RNA-seq files on the usegalaxy.org server. There are a few tools required for t…

galaxybot
@galaxybot

[unknown]
Average out duplicate rows and created a new file [usegalaxy.org support]
Hi Everyone,

I am new to galaxy and thus wanted to get some inputs. I have a microarray file with gene names as rows and corresponding samp…

galaxybot
@galaxybot
[unknown]
Issue with Cloudlaunch can't launch Galaxy on AWS [Uncategorized]
Trying to launch a Galaxy instance (Genomics Virtual Lab) on Amazon Web Services using Cloudlaunch. I set up an AWS account but was having r…
manojmw
@manojmw

Hello everyone,

I am trying to install Galaxy (Version - 20.09) locally through the terminal on macOS. After installing and creating a virtual environment, I tried to run Galaxy locally using sh run.sh command.

But I am getting this error -

thunder lock: disabled (you can enable it with --thunder-lock)

probably another instance of uWSGI is running on the same address

bind(): Address already in use [core/socket.c line 769]
I am not getting any URL in the terminal so that I can run it locally. I uninstalled Galaxy, installed it in a different location, and repeated the process several times. I also searched online forums for the solution but could not find any. I am still not able to run Galaxy locally. Any suggestions or help would be greatly appreciated.

Thank you.

Nicola Soranzo
@nsoranzo
@manojmw It seems you already have something using the port that Galaxy wants to use (8080 by default IIRC).
Either kill the process using that port or change the port for Galaxy in config/galaxy.yml
galaxybot
@galaxybot

[unknown]
Memory allocated exceeded error [usegalaxy.org support] error
Hi,

I’m trying to use the classify.seqs() function from mothur using a non-standard reference database obtained from OTUX - https://web.rn…

manojmw
@manojmw
@nsoranzo ....Thank you very much!...... I will check it and let you know
manojmw
@manojmw
Thank you so much! @nsoranzo ....I found the process using port 8080 and killed the process. Now, it is working.....cheers:)
tensionhead
@tensionhead
Hello, I tried to run a fresh clone of Galaxy 20.09 and ran into this error after ./run.sh:
*** uWSGI is running in multiple interpreter mode ***
spawned uWSGI worker 1 (and the only) (pid: 151751, cores: 4)
spawned 2 offload threads for uWSGI worker 1
Exception ignored in: <function _after_at_fork_child_reinit_locks at 0x7f7e6d16a160>
Traceback (most recent call last):
  File "/usr/lib/python3.8/logging/__init__.py", line 260, in _after_at_fork_child_reinit_locks
    _releaseLock()  # Acquired by os.register_at_fork(before=.
  File "/usr/lib/python3.8/logging/__init__.py", line 228, in _releaseLock
    _lock.release()
RuntimeError: cannot release un-acquired lock
ok, but if I ./run.sh again galaxy starts up, so I guess it's nothing critical in the end?!
miguensblanco
@miguensblanco
Hi guys, I am bit out of my depth here. I want to reanalyse data from a paper that I have seen (total size 60Gb) . I've upload the data from a SRA file to Galaxy, I have check QC, trimmed and interlace the data. Problem is when I am trying to do the assembly (Unicycler), I did run out of memory by quite a lot, I have already 308 Gb of memory in my disk and the work have been paused because the memory issue. Maybe I am not understanding the concept of Galaxy properly, maybe is for smaller datasets,etc. Is that right? Thanks!
tensionhead
@tensionhead
@miguensblanco the unicycler tool is limited to 80Gb of RAM on usegalaxy.eu is that the galaxy instance you are using?
miguensblanco
@miguensblanco
I am using Galaxy Main (usegalaxy.org) but actually my problem is with the disk quota. I have try to remove everything except the files needed to run the assembly of my samples but I am going above 300 GB. Any tip will be really appreciate, thanks!
Björn Grüning
@bgruening
@miguensblanco please log out and log in again
and make sure you have purged the datasets
miguensblanco
@miguensblanco
@bgruening Yes, I was aware of that. As I mention above, I was even tracking the memory since I have issues at the beginning of the analysis, but now looks like I always go over the limit when I am doing the assembly. I think is quite likely that I am doing the wrong type of assembly for these samples
manojmw
@manojmw

Hello everyone,
I am trying to map a sample sequence to the human reference genome (GRCh38). I am using BWA-MEM (>100 bp) tool. I have loaded my sample data (format: Fastq-Sanger) into the galaxy, as well as the reference genome from the UCSC main table browser. The reference genome is in tabular format...I also tried loading a fasta format of the reference genome.

When I try to map the sample sequence to the reference genome, I am not getting an option to select the reference genome under -[ Select reference genome sequence dropdown]. As a result, I am not able to map the sequence. I really need assistance.

Any suggestions or help would be greatly appreciated.

Thank you.

Cristóbal Gallardo
@gallardoalba
Hi @manojmw, the BWA-MEM tool allows you to load the human reference genome directly from the built-in index.
Screenshot from 2020-11-30 11-57-12.png
manojmw
@manojmw
Thank you @gallardoalba for the response. I am running Galaxy locally and as I mentioned earlier, no options were available to me in the drop-down menu. Then, I downloaded the reference genome from NCBI and loaded the custom FASTA format of this reference genome into Galaxy, and Normalized the data using the NormalizeFasta tool. Then, it finally worked and I was able to map the sample data to the reference genome.
huar17
@huar17
Hello! I am trying to use RNA STAR using A. thaliana as the reference genome. However, it is not listed and I was told to "contact the Galaxy team (--genomeDir)." Where should I go to do that?
Nicola Soranzo
@nsoranzo
@huar17 Which server are you using? The index should be available on https://usegalaxy.eu/
huar17
@huar17
@nsoranzo I am using the main server (usegalazy.org)
**usegalaxy.org
Nicola Soranzo
@nsoranzo
I am not an admin on either, so cannot really help you. You can either move to .eu or upload the A. thaliana reference genome to .org and change the "Custom or built-in reference genome" select box to use the FASTA dataset from your history.
Nolan Woods
@innovate-invent
@huar17 try uploading a custom build (under the user menu)
huar17
@huar17
@nsoranzo @innovate-invent thank you!
galaxybot
@galaxybot

[unknown]
Need help with selecting reference genome in Galaxy installed locally [usegalaxy.org support] admin, galaxy-local, reference-annotation, reference-genome
Hello everyone,

I am trying to annotate a VCF file containing the sample data to predict the genes with polymorphic sites. I am using ANNOV…

MaralQ
@MaralQ
Need help with DE analysis using limma-voom
I keep getting this error: Fatal error: Exit code 1 ()
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
line 2 did not have 4 elements
Calls: read.table -> scan
Execution halted
Nolan Woods
@innovate-invent
@MaralQ check the input, my guess is that it is expecting 4 columns but only getting two
galaxybot
@galaxybot
[unknown]
Uploading A. thaliana reference genome to RNA STAR [usegalaxy.org support] input, genome, rna-star, reference-genome
I am using RNA STAR for analyzing paired-end Arabidopsis RNA data, however, the Arabidopsis genome is not one of the built-in reference geno…
MaralQ
@MaralQ
@innovate-invent Thanks. Which one? I have provided 3 files, the factordata, the countdata and the annotdata. The factor data contains 3 columns, the annotdata also contains 3 columns, and the count data contains 17 columns.
miguensblanco
@miguensblanco
Hi guys, I am assembly my metagenomic reads with MEGAHIT in usegalaxy.org . After an hour into the run I am getting an error message because the job used more memory that it is allocated . I think this time is related to the RAM memory, not sure anyway. Any ideas? Thanks!
galaxybot
@galaxybot
[unknown]
Get selected reads from SRA data sets [usegalaxy.org support] fastq, sra, filter
I want to retrieve a subset of FASTQ reads from SRA data sets in my History. Previously, I used fasterq-dump to import 4 SRA data sets into …
galaxybot
@galaxybot

[unknown]
0 count with both featureCount or htseq_count [Uncategorized]
Dear community,

I am writing that post after several days of researches.

My aim seemed simple because It’s sounds to me like a habits for …

galaxybot
@galaxybot
[unknown]
makeblastdb: error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory [Uncategorized]
Tried to make nucleotide database from a fasta file with multiple as well as single large sequence. Neither worked. I either get the duplica…
Björn Grüning
@bgruening
For all interested in GitHub actions: https://mg.pov.lt/blog/switching-to-github-actions.html
galaxybot
@galaxybot

[unknown]
error when using several factors in deseq2 [usegalaxy.org support]
Hi,

I am having an issue using DESeq2 at usegalaxy.org

I have an RNA-seq using data from the litterature, I aligned using Hisat2 and made …

galaxybot
@galaxybot

[unknown]
Filter GTF attributes by a list of attributes [usegalaxy.eu support]
I have a GTF that looks like this with 2 000 000 rows:

[Capture d’écran 2020-12-02 à 10.49.33]

I now want to filter it with a list of t…

galaxybot
@galaxybot
[unknown]
too much time for start a job? [usegalaxy.org support]
I have sent two jobs to Trinity, on November 28 and 29 respectively. I have read in the Galaxy Help that machines are rather busy, but I won…
galaxybot
@galaxybot
[unknown]
DE analysis after StringTie [Uncategorized] stringtie
I’ve been working on a single cell RNA-seq dataset (SMARTSeq, Nextera libraries) with RNASTAR and StringTie, and have visualised the total d…
saeed
@pshtiwan
hI
I want to mapping my raw data (.fastq ) against to ref genome and annotation gtf file. But the genome which I interested (Streptomyces coelicolor) it is not in the list. Kindly, can add the fasta and gtf(gff) to list.
@galaxybot
saeed
@pshtiwan
@galaxybot
Hi
I want to mapping my raw data (.fastq ) against to the ref genome and annotation gtf file. But the genome which I interested (Streptomyces coelicolor) it is not in the list. Kindly, can add the fasta and gtf(gff) to list.