nanoporetech/epi2me-api

API for communicating with the EPI2ME Platform for nanopore data analysis. Used by EPI2ME Agent & CLI.

epi2me-api's Issues

Couldn't start Fasta reference workflow

router.post('/fastqref', function (req, res, next) {
  const EPI2ME = new API({
    url: 'https://epi2me.nanoporetech.com',
    apikey: 'apikeyhere',
    apisecret: 'secretkeyhere',
    inputFolder: req.body['inputFolder'],
    outputFolder: req.body['outputFolder'],
  });

  const factory = new Factory(API);
  const workflowId = 1825;
  EPI2ME.REST.startWorkflow({ variables: { idWorkflowInstance: workflowId }})
  .then(console.info)
  .catch(console.error);

Error is attached below.

epi2me-api documentation

We want to run other workflows other than Fastq custom alignment (id: 1825). We want to know when will the documentation be ready? As, we are on a tight schedule to integrate epi2me-api with our program. If the documentation won't be ready soon, Can you help us with syntax?

File uploading fails: NoSuchBucket error

It started the analysis but we have an issue with uploading the files.

LIVE INSTANCE STATE { download: { progress: { bytes: 0, total: 0, niceSize: 0 }, success: { files: 0, bytes: 0, reads: 0, niceReads: 0, niceSize: 0 }, types: {}, fail: 0, niceTypes: '' }, upload: { progress: { bytes: -8655034949, total: 0, niceSize: '-8655034949' }, success: { files: 0, bytes: 0, reads: 0, niceReads: '0', niceSize: '0' }, types: {}, filesCount: 29, niceTypes: '', failure: { 'NoSuchBucket: The specified bucket does not exist': 28 } }, warnings: [] }

When we try to upload files, it give the above error. Can you help us with how to specify the files to the api?

Originally posted by @youssefabadir in #2 (comment)

Error while downloading output file from epi2me-api (fastq custom alignment workflow)

I am trying to run fastq custom alignment workflow and it download this file instead of the output files.

telemetry-252547.log

Is this a problem from my side?

epi2me-agent3-promethion (Ubuntu)

Apologies but I didn't find the right place to mention an error I obtained when trying to install the agent for epitome service as described in:

https://community.nanoporetech.com/docs/prepare/library_prep_protocols/epi2me/v/mte_1014_v1_revca_11apr2016/installing-the-desktop-age-50426

It seems the newest version (3.4.1-5831769) gives an error installation (or updating for that matter) in ubuntu., e.g.:
sudo apt-get install epi2me-agent3-promethion
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following NEW packages will be installed:
epi2me-agent3-promethion
0 upgraded, 1 newly installed, 0 to remove and 57 not upgraded.
Need to get 80.8 MB of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 https://cdn.oxfordnanoportal.com/apt focal-stable/non-free amd64 epi2me-agent3-promethion all 3.4.1-5831769 [80.8 MB]
Fetched 80.8 MB in 6s (13.1 MB/s)
Selecting previously unselected package epi2me-agent3-promethion.
(Reading database ... 398624 files and directories currently installed.)
Preparing to unpack .../epi2me-agent3-promethion_3.4.1-5831769_all.deb ...
Unpacking epi2me-agent3-promethion (3.4.1-5831769) ...
Setting up epi2me-agent3-promethion (3.4.1-5831769) ...
id: ‘grid’: no such user
id: ‘prom’: no such user
chown: invalid user: ‘dummy’
chown: invalid user: ‘dummy’
chgrp: invalid group: ‘dummy’
Migrating Agent data out of $home into /data
ln: failed to create symbolic link '~dummy/.epi2me': No such file or directory
chown: invalid user: ‘dummy’
chgrp: invalid group: ‘dummy’
dpkg: error processing package epi2me-agent3-promethion (--configure):
installed epi2me-agent3-promethion package post-installation script subprocess returned error exit status 1
Processing triggers for mime-support (3.64ubuntu1) ...
Processing triggers for hicolor-icon-theme (0.17-2) ...
Processing triggers for gnome-menus (3.36.0-1ubuntu1) ...
Processing triggers for desktop-file-utils (0.24-1ubuntu3) ...
Errors were encountered while processing:
epi2me-agent3-promethion
E: Sub-process /usr/bin/dpkg returned an error code (1)

In my opinon, the subprocess of installation (through dpkg) assumes that the system have two users called grid and prom and even a group called dummy.

Anyway, is this the right place to report this error? Otherwise, could you please point me to the right place?

Thank you!

Amhed

wf-metagenomics request

Hello,
We are starting with the study of resistance genes, and we are using EPI2ME Desktop and we were very happy because it provided a lot of information very useful. However, if we comparing EPI2ME Agent vs EPI2ME Desktop, EPI2ME Agent analysis Fastq Antimicrobial Resistance showed the taxon to which the resistance gene belongs and the ontolology of the resistance gene, but we can see that this option isn’t in EPI2ME Desktop wf-metagenomics. Is it planned to have these options a nearer future, please?

We are looking forward to hearing from you.

Thank you!

apptainer to execute nextflow

I am trying to run epi2me on an HPC but keep running into nextflow trying to run through docker instead of apptainer. I added apptainer to the profile list (see below) but it will not run
profiles {
// the "standard" profile is used implicitly by nextflow
// if no other profile is given on the CLI
standard {
docker {
enabled = true
// this ensures the container is run as the host user and group, but
// also adds the host user to the within-container group
runOptions = "--user $(id -u):$(id -g) --group-add 100"
}
}

// using singularity instead of docker
singularity {
singularity {
enabled = true
autoMounts = true
}
}

// using Apptainer instead of Docker
apptainer {
apptainer {
enabled = true
autoMounts = true
container = "/path to /nextflow_latest.sif"
}
}