Failed to install-deps

[Gyzele]

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:

• snap:1.0dev.96
• salmon:0.6.0
• blastplus:2.2.[0-9]
  Why does it happen?

[abshah]

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

[blahah]

to do that:

gem install transrate -s https://github.com/abshah/transrate

[Shellfishgene]

@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]

@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]

@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]

@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]

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]

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]

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]

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]

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:

• salmon:0.6.0
• blastplus:2.2.[0-9]
  (trenv) martin.tesicky@azor:~/Transrate/training_data/example_data$

I would be very grateful for resolving this issue.

Kind Regards,
Martin Tesicky

[JVRoigG]

Hi,

Has anyone solved this issue?

[ndaluthge]

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.

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]

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