8
votes
tRNAscan-SE error: FATAL: Unable to find /usr/local/bin/cmsearch executable
You may try to set the correct path through the infernal_dir variable in tRNAscan-SE.conf.src. You might need to do this before ...
- 3,100
6
votes
Cannot install chromosomer
Chromosomer only exists for Python 2. You should thus be able to install it via
pip2 install chromosomer
But:
Your Python installation is a bit screwed up: ...
- 4,845
5
votes
Accepted
tRNAscan-SE error: FATAL: Unable to find /usr/local/bin/cmsearch executable
An easy way to build tRNAscan and their dependencies "all Infernal packages" without confusion is to run
conda install -c bioconda trnascan-se
- 374
4
votes
tRNAscan-SE error: FATAL: Unable to find /usr/local/bin/cmsearch executable
tRNAscan-SE 2.0 requires separate installation of Infernal 1.1.2.
The source code and prebuilt binaries can be obtained at
http://eddylab.org/infernal/.
The installation directory of Infernal should ...
- 41
4
votes
Accepted
Psipred installation
Try with:
makeblastdb -in uniref90.fasta -dbtype prot -input_type fasta -out uniref90
The -out is the name of the DB. So if ...
- 323
4
votes
Problem installing last build of Sniffles
You need to install GCC, or a newer version of Clang.
Your compiler — though the binary is called gcc — is actually Clang, and the Clang version that’s shipping ...
- 4,845
4
votes
Accepted
How to use busco installed through conda?
From the README, it looks like the command-line entry point is not busco but run_BUSCO.py. This seems to agree with the bioconda ...
- 5,060
4
votes
Error in PSI-BLAST when running psipred locally
This error could be due to the fact that you are using legacy blast, have you tried using BLAST+ instead?
If you wish to use PSIPRED with BLAST+, then use the runpsipredplus script
here, rather than ...
- 63
4
votes
Installing DESeq2 in Ubuntu
First I installed this libraries:
sudo apt-get install libcurl4-openssl-dev libxml2-dev
I then installed RCurl:
...
- 645
4
votes
bcl2fastq2 v2.20.0 converstion software on Ubuntu 18.04
Install it with conda.
conda install -c dranew bcl2fastq
- 41
3
votes
Accepted
TRAL does not find "Phobos result file"
TRAL 0.3.5 has bugs running and parsing Phobos. You can follow progress towards a fix on this issue: https://github.com/acg-team/tral/issues/16
Until the issue is fixed, you should remove Phobos from ...
- 146
3
votes
Error compiling HMMER v3.2.1
I would strongly recommend to use Bioconda instead of compiling. It is one of the channels ("distributors of packages") in Anaconda Cloud which is basically a package source for conda.
In short - ...
- 130
3
votes
Unable to install bedtools on windows 10 ubuntu
My personal advice would be to avoid compiling tools like this if you can avoid it, especially where you are using a "barebones" setup like the one you get with WSL Ubunutu as you'll almost always run ...
- 3,301
3
votes
Accepted
Problem installing RATT
Usually the home of a program is where the executable is. In order to make the system aware you need to include it as a variable when the terminal is run.
So you need to add it to the file at ...
- 4,693
3
votes
Accepted
How to install blasr on Mac OS X?
The path of least resistance is probably to run the software inside a container. If you install docker, you can just do the following:
...
- 1,816
3
votes
Master of Pores Installation Mac OS Mojave 10.14
you should not move nextflow within ~/master_of_pores/NanoPreProcess/bin .
Just add nextflow in your path.
...
- 31
2
votes
Albacore wheel not supported on this platform (Mac OS X El Capitan)
Not sure about conda as I don't use it, but I can highly recommend pipenv which is the python.org recommended package management ...
- 663
2
votes
Accepted
Does MinKNOW work with Mac OSX high sierra 10.13.1?
Some replies from ONT is:
OS X is supported and you can view the installation instructions on
our Downloads page linked below. At the moment High Sierra is not
officially supported as we have ...
- 2,459
2
votes
How to install blasr on Mac OS X?
I've had many issues with installing blasr on my own, but it's a breeze using (bio)conda, see https://anaconda.org/bioconda/blasr
conda install -c bioconda blasr
- 1,314
2
votes
tRNAscan-SE error: FATAL: Unable to find /usr/local/bin/cmsearch executable
A much cleaner solution is given in @bli's answer.
The error message is telling you that tRNAScan-SE is looking for the cmsearch executable at ...
- 9,662
2
votes
Unable to install bedtools on windows 10 ubuntu
make1: g++: Command not found
You do not have g++ installed on your machine. This is used to compile the bedtools into an executable file.
Here is a tutorial on installing g++
- 2,574
2
votes
Why can I not install snakemake on my SLURM computer even though I can find it in the bioconda channel?
I created a file .condarc in my home directory with the following content:
channels:
- conda-forge
- bioconda
- defaults
and it works now. I don't ...
- 2,459
2
votes
R studio failed to install the latest development version of hdf5r from Github (win10)
Try running this:
source("https://bioconductor.org/biocLite.R")
biocLite("hdf5r")
Just a different method of installing packages besides github. It is more ...
- 836
2
votes
Accepted
Repeatscout installation problem
If you're in the RepeatScout directory you need to execute the Perl script with a ./ prefix, like so.
...
- 5,060
2
votes
Accepted
How can I run the fdnadist command from the EMBOSS package?
To find emboss packages type wossname, then hit enter twice. You will see all the programs. There is one called ...
- 527
2
votes
How can I run the fdnadist command from the EMBOSS package?
I found fdnadist in embassy-phylip package https://anaconda.org/bioconda/embassy-phylip
- 21
2
votes
How do I install hammock?
Download a release (Hammock_v_1.2.0.7z) from https://github.com/krejciadam/hammock/releases
Unzip
To run the first example:
...
- 56
2
votes
Accepted
the following errors are found during the installation of an open source software, UNCeqR on z shell
It is a Perl compilation error:
(Perl libraries) Math::CDF-0.1 -- Generate probabilities and quantiles from several
statistical probability functions
conda install -c bioconda perl-math-cdf
cpan ...
- 239
2
votes
Only top scored, non community-wiki answers of a minimum length are eligible