Comments (12)
Hello @francesconardi,
TransPi now uses individual conda environments for each process. This is because it was having issues when updating packages and working in a single environment. After you clone TransPi and have the databases, you only need to specify -profile conda
and the pipeline will handle the creation of the environments for you. That is why it is not using the transpi_env.yml
anymore. However, I still have that part in the precheck code (removing soon).
The main issue I see here is that the precheck is not successfully working for the version check of conda. Thanks for pointing that out. I'll make a quick edit so you can continue with the installation. Let me know if you have further issues or questions.
Best,
Ramón
from transpi.
I made the change. See 556c2ec
from transpi.
Dear Ramon,
thanks for your quick fix. One step further.
Once the script gets to the point of building the trinotate database (your function trisql_c()), it actually tries to activate an environment named 'TransPi' that is not there (and there should not be, following your previous note). Hence an error. Can you suggest how this can be circumvented?
Thanks indeed
Francesco
from transpi.
Hello,
I just merged the dev branch with the master. In the dev I already fixed this issue (see #29 ). Anything ket me know
Best,
Ramón
from transpi.
Dear Ramon,
I am slowly working my way with the installation, manually completing some steps that fail in automatic.
Creation of some conda envs failed, and I could rescue the process by issuing the create environment command manually and then resuming the run.
I am now at the rnaquast env, whose install command is:
conda create --mkdir --yes --quiet --prefix /home/u3601/prog/TransPi_folder/condaEnv/env-fa8b0a403402a49160ee9bce39b0a3c5 -c conda-forge bioconda::rnaquast=2.0.1=0
The command fails both when issued in the context of the nextflow pipeline (it trows an error) and ALSO if I issue the command manually (unlilke other envs).
Can you suggest a workaround to install rnaquast env, possibly in the same env structure created by TransPi?
Thanks
Francesco Nardi
from transpi.
Hello @francesconardi,
Sometimes there are issues with conda packages if you already have them. One thing you can try is to use the conda clean --all
to erase all packages and info of conda. Then start again the pipeline. Let me know if that works.
Best,
Ramón
from transpi.
Hi Ramon,
I have succesfully cloned the rnaquast env from a different source:
conda create --mkdir --prefix /...../condaEnv/env-fa8b0a403402a49160ee9bce39b0a3c5 -c bioconda rnaquast=2.0.1=0
and, at present, the main line of TransPi is running smootly.
I'm now after the three external packages SignalP, tmhmm and rnammer, where I get some errors.
I see that signalp expects input using a different set of options compared to what TransPi issues. I am wondering if this depends on the package version I downloaded. Before I try to edit the nextflow script accordingly, could you indicate the exact version of the three packages you are using (I'm on centos linux). This may be a simple solution.
Cheers,
and thanks for your continuing assistance,
Francesco Nardi
from transpi.
Hello @francesconardi,
No worries at all. Thank you for pointing these issues so I can come with solutions for future updates.
Good to hear the env was created successfully.
For the signalP analysis I am using version 4.1.
Best,
Ramón
from transpi.
May I know which versions of rnammer and tmhmm you are using as well?
Thank you
Francesco Nardi
from transpi.
RNAmmer v1.2 and TMhmm v2.0. What errors do you get?
from transpi.
Dear Ramon,
I am working on the integration of Rnammer, SignalIP and tmhmm with the main script, and I get a number of errors.
The one I am looking into at present arises from the script (apparently) not finding RnammerTranscriptome.pl (output below).
I actually have two copies of the script:
~/prog/TransPi_folder/scripts/RnammerTranscriptome.pl
~/prog/TransPi_folder/condaEnv/env-b96eed500b8c9d678c4cc5d666983118/bin/RnammerTranscriptome.pl
Where is TransPi looking for the aforementioned script? Where is it expected to be?
Thank you,
Francesco Nardi
(output)
Command output:
-- Starting with RNAMMER --
-- Done with RNAMMER --
Command error:
.command.sh: line 7: RnammerTranscriptome.pl: command not found
from transpi.
Hello,
You need to provide the PATH of these programs in the config file. We do this in the pipeline since each user needs a license for using the tools. Once you have the PATH in the config you should be fine
TransPi/template.nextflow.config
Lines 45 to 51 in 146e71c
from transpi.
Related Issues (20)
- Error in rRNAfilter and sortmerna
- KEGG warn message HOT 3
- Error Running Full Analysis: Process `fastp (1_R1)` terminated with an error exit status (255) HOT 5
- Process `fastp (Ccelos_S1_L001)` terminated with an error exit status (127) HOT 1
- Transdecoder cannot be found
- Signal P Compatibility Error? HOT 2
- Process fastp (AC422_S687_S14_L001_R) terminated with an error exit status (1)
- Unexpected run time, Trinity/salmon HOT 1
- Process requirement exceed available memory
- problems running full analysis (--all option) and evigene's script
- Operator `into` has been deprecated -- it's not available in DSL2 syntax
- Trinotate preparation step in Precheck script silently fails with missing Perl module
- Missing transpi_env.yml HOT 2
- Uniprot Metazoan database not downloaded due to changes in UniProt REST API HOT 2
- TransPi on HPC failing to pull singularity image HOT 3
- Error executing process > 'transdecoder_predict HOT 1
- line 8: insilico_read_normalization.pl: command not found HOT 5
- Fail to download uniprot_metazoa_33208.fasta HOT 4
- Can I inform the direction of sequencing? HOT 1
- issue of onlyAnn mode
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from transpi.