Salmon installation error

Question

[kousi31]

Hi all.

I am trying to install salmon-0.13.0.

tar -zxvf salmon-0.13.0.tar.gz
cd salmon-0.13.0
mkdir build
cd build
cmake -DFETCH_BOOST=TRUE ..
make

I got the following error:

boost_1_66_0.tar.gz: FAILED
sha256sum: WARNING: 1 computed checksum did NOT match
boost_1_66_0.tar.gz did not match expected SHA256! Exiting.
CMakeFiles/libboost.dir/build.make:90: recipe for target 'libboost-prefix/src/libboost-stamp/libboost-download' failed
make[2]: *** [libboost-prefix/src/libboost-stamp/libboost-download] Error 1
CMakeFiles/Makefile2:72: recipe for target 'CMakeFiles/libboost.dir/all' failed
make[1]: *** [CMakeFiles/libboost.dir/all] Error 2
Makefile:162: recipe for target 'all' failed
make: *** [all] Error 2
  

Before trying this cmake -DFETCH_BOOST=TRUE .. , I downloaded boost from wget -O boost_1_55_0.tar.gz http://sourceforge.net/projects/boost/files/boost/1.55.0/boost_1_55_0.tar.gz/download

tar xzvf boost_1_55_0.tar.gz
cd boost_1_55_0/
sudo apt-get update
sudo apt-get install build-essential g++ python-dev autotools-dev libicu-dev build-essential libbz2-dev
./bootstrap.sh --prefix=/usr/local
user_configFile=find $PWD -name user-config.jam
echo "using mpi ;" >> $user_configFile

I found a solution in this link. But I am unable to understand it properly. I understand I have to edit CMakelist.txt, but I couldn't understand which line to replace with what. But there is no CMakeLists.txt in the build folder.

Thank you for your help in advance!

Answer 1

[Devon Ryan]

Make sure you include the conda-forge channel for dependency resolution:

conda create -n salmon -c conda-forge -c bioconda salmon

[kousi31]

Thank you all for your suggestions.

With conda create -n salmon -c conda-forge -c bioconda salmon

The following NEW packages will be INSTALLED:

bzip2 conda-forge/linux-64::bzip2-1.0.6-h14c3975_1002
icu conda-forge/linux-64::icu-58.2-hf484d3e_1000
jemalloc conda-forge/linux-64::jemalloc-5.2.0-he1b5a44_0
libboost pkgs/main/linux-64::libboost-1.67.0-h46d08c1_4
libgcc-ng pkgs/main/linux-64::libgcc-ng-8.2.0-hdf63c60_1
libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-8.2.0-hdf63c60_1
salmon bioconda/linux-64::salmon-0.13.1-h86b0361_0 tbb
conda-forge/linux-64::tbb-2019.5-hc9558a2_0 xz
conda-forge/linux-64::xz-5.2.4-h14c3975_1001 zlib
conda-forge/linux-64::zlib-1.2.11-h14c3975_1004

I think version 0.13.1 is getting installed :)

[LPDHD86]

Hi Devon,

thanks for the suggestion. I tried to use the exact "conda create" command above in an HPC environment. No error messages, and when I call salmon without any option all looks fine:

~/.conda/envs/salmon/bin/salmon 
salmon v0.14.0
Usage:  salmon -h|--help or 
        salmon -v|--version or 
        salmon -c|--cite or 
        salmon [--no-version-check] <COMMAND> [-h | options]
Commands:
     index Create a salmon index
     quant Quantify a sample
     alevin single cell analysis
     swim  Perform super-secret operation
     quantmerge Merge multiple quantifications into a single file

However, with a specific command like this one

~/.conda/envs/salmon/bin/salmon alevin -h

it keeps working forever without printing anything. I guess something has gone wrong, but I am not sure what I should check?

[Devon Ryan]

Perhaps your cluster is having issues. Close the terminal, reconnect and try again. BTW, you'll want conda activate salmon to activate the environment, then you don't need to give the full path.

Answer 2

[waqaskhokhar999]

If you have conda, you can use this command to install salmon (https://anaconda.org/bioconda/salmon):

conda install -c bioconda salmon

[kousi31]

Thank you for your reply.

I initially installed with `conda install -c bioconda salmon. But the version that got installed was 0.8.1. But trinity requires salmon version 0.9 or above. conda upgrade also did not work.

[waqaskhokhar999]

You need to update conda, use this command to update conda packages:

https://docs.conda.io/projects/conda-build/en/latest/install-conda-build.html#updating-conda-and-conda-build

conda update conda

[kousi31]

Some of the command outputs..

conda update conda

Collecting package metadata: done
Solving environment: done

# All requested packages already installed

conda update salmon

Collecting package metadata: done
Solving environment: done

# All requested packages already installed.

conda --version
conda 4.6.14

salmon --version
version : 0.8.1

[WouterDeCoster]

The version on bioconda is v0.13.1, so it's odd that you got 0.8.1. Make sure you don't have a second salmon installation somewhere on your $PATH. See if which salmon shows it is in an anaconda/miniconda directory.

Even better would be to use a separate environment:

conda create -n salmon -c bioconda salmon

[kousi31]

Some of the outputs..

conda create -n salmon -c bioconda salmon

Collecting package metadata: done Solving environment: done

## Package Plan ##

environment location: /home/nbagr/miniconda3/envs/salmon

added / updated specs:
  - salmon

   The following NEW packages will be INSTALLED:

salmon             bioconda/linux-64::salmon-0.8.1-0
 Proceed ([y]/n)?

It is trying to download 0.8.1 again I guess..

which salmon

/home/nbagr/miniconda3/bin/salmon

Answer 3

[20190634]

A query, after applying the "conda activate salmon" commands * I have a problem when I run the other softwares The command "sudo" is available in "/ usr / bin / sudo" The command could not be found because "/ usr / bin" is not included in the PATH environment variable.

How could I disable salmon.

[WouterDeCoster]

Why do you need sudo?

conda activate salmon activates an environment in which you install(ed) salmon. You can deactivate it using, well, conda deactivate.