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blahah / transrate

Understand your transcriptome assembly
http://hibberdlab.com/transrate
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Failed to install-deps #240

Open Gyzele opened 4 years ago

Gyzele commented 4 years ago

I tried to install the transrate deps, but the installation failed. transrate --install-deps all Checking dependencies Installing snap (1.0dev.96)... Installing salmon (0.6.0)... Installing blastplus (2.2.[0-9])... [ERROR]Failed to install:

abshah commented 4 years ago

Hi @Gyzele , can you try using this fork and let us how it works for you.

blahah commented 4 years ago

to do that:

gem install transrate -s https://github.com/abshah/transrate
Shellfishgene commented 3 years ago

@abshah The deps file in your fork contains the old download link for Salmon. @blahah That does not actually work for me. This works:

gem install specific_install
gem git_install https://github.com/abshah/transrate
abshah commented 3 years ago

@Shellfishgene, I can test it out with latest version of Salmon (ver. 1.4.0), and let you know if the this version works better.

Shellfishgene commented 3 years ago

@abshah I meant there is a conflict in your deps file, the version check is for 0.13.0 but the download link is for 0.6.0, here.

But if you want to update it you can also check snap, there is now a version 1.0.0. While you're at it you might also want to switch out the trollop module to optimist to get rid of the warning, it seems to be a drop-in replacement.

abshah commented 3 years ago

@Shellfishgene , updated the Salmon link.

Thanks for spotting that.

I will also check the latest versions of SNAP and Salmon, and fix the trollop module to optimist, in the next few days.

Rhinogradentia commented 3 years ago

Hi, I got the same error as above and used the workaround

  gem install specific_install
  gem git_install https://github.com/abshah/transrate
  transrate --install-deps all

, but now the blast+ installation fails which was successful before.

+ transrate --install-deps all
[DEPRECATION] The trollop gem has been renamed to optimist and will no longer be supported. Please switch to optimist as soon as possible.
Checking dependencies
Installing snap (1.0dev.96)...
Installing bam-read (1.0.0)...
Installing salmon (0.13.0)...
Installing blastplus (2.2.[0-9])...
/var/lib/gems/2.7.0/gems/transrate-1.0.3/bin/transrate:13:in `raise': There was a problem unpacking ncbi-blast-2.2.29+-x64-linux.tar.gz (RuntimeError)

gzip: stdin: invalid compressed data--format violated
tar: Unexpected EOF in archive
tar: Unexpected EOF in archive
tar: Error is not recoverable: exiting now

What could help here? Thank you Best, Nadine

Shellfishgene commented 3 years ago

It tries to install blast from here: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.29/ncbi-blast-2.2.29+-x64-linux.tar.gz (on Linux). You can check if you can download this manually or if there is some error. You can also install it manually instead of through transrate.

Rhinogradentia commented 3 years ago

Thanks - now I get another error - maybe I will have a look at the source myself:

Setting up ruby-dev:amd64 (1:2.7+1) ...
Processing triggers for libc-bin (2.31-0ubuntu9.1) ...
+ gem install specific_install
Successfully installed specific_install-0.3.5
Parsing documentation for specific_install-0.3.5
Installing ri documentation for specific_install-0.3.5
Done installing documentation for specific_install after 0 seconds
1 gem installed
+ gem git_install https://github.com/abshah/transrate
/usr/bin/git
http installing from https://github.com/abshah/transrate
Cloning into '/tmp/d20210113-4381-1iaq8j0'...
/usr/lib/ruby/2.7.0/rubygems/ext/builder.rb:165: warning: conflicting chdir during another chdir block
  Successfully built RubyGem
  Name: transrate
  Version: 1.0.3
  File: transrate-1.0.3.gem
!    The 'trollop' gem has been deprecated and has been replaced by 'optimist'.
!    See: https://rubygems.org/gems/optimist
!    And: https://github.com/ManageIQ/optimist
Building native extensions. This could take a while...
/usr/lib/ruby/2.7.0/rubygems/ext/builder.rb:173: warning: conflicting chdir during another chdir block
Successfully installed
+ transrate --install-deps all
Checking dependencies
Installing snap (1.0dev.96)...
Installing bam-read (1.0.0)...
Installing salmon (0.13.0)...
Installing blastplus (2.2.[0-9])...
FATAL:   While performing build: while running engine: exit status 1
Shellfishgene commented 3 years ago

No idea what causes that, if you don't want to mess with it you could also try using the biocontainers container for transrate, if you can use docker or singularity.

MartinTes commented 3 years ago

Hi,

I have recently installed the latest version of Transrate using bioconda and I might encounter the similar issue:

conda create -n trenv -c conda-forge/label/cf202003 ruby conda activate trenv conda install -c bioconda transrate

When I run it with the example dataset (transrate --assembly transcripts.fa/) I had the following call:

[ INFO] 2021-03-15 13:39:24 : Loading assembly: /home/martin.tesicky/Transrate/training_data/example_data/transcripts.fa [ INFO] 2021-03-15 13:39:24 : Analysing assembly: /home/martin.tesicky/Transrate/training_data/example_data/transcripts.fa [ INFO] 2021-03-15 13:39:24 : Results will be saved in /home/martin.tesicky/Transrate/training_data/example_data/transrate_results/transcripts [ERROR] 2021-03-15 13:39:24 : could not find snap in the path (trenv) martin.tesicky@azor:~/Transrate/training_data/example_data$

Based on that I decided to install dependencies but I have got another warning: transrate --install-deps

(trenv) martin.tesicky@azor:~/Transrate/training_data/example_data$ transrate --install-deps all [DEPRECATION] This gem has been renamed to optimist and will no longer be supported. Please switch to optimist as soon as possible. Checking dependencies Installing snap (1.0dev.96)... Installing salmon (0.6.0)... Installing blastplus (2.2.[0-9])... [ERROR] 2021-03-15 13:21:22 : Failed to install:

I would be very grateful for resolving this issue.

Kind Regards, Martin Tesicky

JVRoigG commented 3 years ago

Hi,

Has anyone solved this issue?

ndaluthge commented 3 years ago

Probably this might help - I was getting the 'Failed to install:' error for 'salmon (0.6.0)'. When I opened the /bin folder in my Transrate env (I run transrate as a Conda env) I could see that 'salmon' was there but apparently it wasn't been recognized. So I deleted salmon from this 'bin' folder and downloaded the salmon binary (version 1.5.2) 'salmon-1.5.2_linux_x86_64.tar' to my desktop, unpacked it, and dragged the salmon executable to the /bin folder of my Transrate Conda env. That seems to have done the trick, and I got transrate to work in 'read-metrics mode' without errors. My guess is that the problem is with the specific salmon (0.6.0) version which transrate tries to download.

dpgrape commented 3 years ago

Hello,

I'm also having this issue. 

transrate --install-deps all
[DEPRECATION] The trollop gem has been renamed to optimist and will no longer be supported. Please switch to optimist as soon as possible.
Checking dependencies
Installing salmon (0.6.0)...
Installing blastplus (2.2.[0-9])...
[ERROR] 2021-10-21 15:59:15 : Failed to install: 
 - salmon:0.6.0
 - blastplus:2.2.[0-9]

I've install transrate (v1.0.3) through conda.

Can anyone help me?

Thank you!

ndaluthge commented 3 years ago

@dpgrape If you go to your conda envs 'bin' folder for transrate, do you see 'salmon' and 'blastplus' as installed packages?

Shellfishgene commented 3 years ago

@dpgrape Try to also install the transrate-tools package in the same conda env. Works for me.

abshah commented 3 years ago

Hello,

I'm also having this issue.

transrate --install-deps all
[DEPRECATION] The trollop gem has been renamed to optimist and will no longer be supported. Please switch to optimist as soon as possible.
Checking dependencies
Installing salmon (0.6.0)...
Installing blastplus (2.2.[0-9])...
[ERROR] 2021-10-21 15:59:15 : Failed to install: 
 - salmon:0.6.0
 - blastplus:2.2.[0-9]

I've install transrate (v1.0.3) through conda.

Can anyone help me?

Thank you!

I can review this over the weekend. Sorry for delayed response.

dpgrape commented 3 years ago

@dpgrape If you go to your conda envs 'bin' folder for transrate, do you see 'salmon' and 'blastplus' as installed packages?

Sorry for the late response. I can see 'salmon' but not 'blastplus' .

@dpgrape Try to also install the transrate-tools package in the same conda env. Works for me.

Thank you, I'll try

ndaluthge commented 3 years ago

Replacing the 'salmon 0.6.0' with 'salmon 1.5.2' in the conda env sorted out the issue with salmon for me. Not sure about the 'blastplus' though. You might have to try downloading that again.

BioinfoAK commented 1 year ago

Hi there, sorry to re-open this thread.

I'm having an issue with installing the dependencies (salmon and blastplus) on an installation of transrate 1.04 from here https://github.com/dfmoralesb/transrate

I've changed links in the deps doc to more recent versions of salmon, unfortunately, that hasn't quite worked.

I'm very new to bioinformatics and code in general, so I'm a bit confused with some of the advice here.

I'd like to install salmon and blastplus manually, but am unsure of where to install them and whether they need to be named in a certain way?

Thanks in advance.

BioinfoAK commented 1 year ago

Hi there, sorry to re-open this thread.

I'm having an issue with installing the dependencies (salmon and blastplus) on an installation of transrate 1.04 from here https://github.com/dfmoralesb/transrate

I've changed links in the deps doc to more recent versions of salmon, unfortunately, that hasn't quite worked.

I'm very new to bioinformatics and code in general, so I'm a bit confused with some of the advice here.

I'd like to install salmon and blastplus manually, but am unsure of where to install them and whether they need to be named in a certain way?

Thanks in advance.

Hi all, just in case someone as clueless as me runs into this fault, I managed to solve this using the following steps:

  1. Download transrate and install according to instructions
  2. Create a conda environment and download all dependencies that are unable to load
  3. manually link them as written https://github.com/pmomadeira/transrate

Hope everyone has a great day!