Questions tagged [software-installation]

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1answer
54 views

How to install/import Biopython into Python 3.8/ PyCharm IDE

I'm new to Python/Biopython programming. I'd like to install Biopython into my PyCharm IDE but I've tried all instructions on this, but it's not confirming it. I have the available biopython file ...
-1
votes
1answer
73 views

Permanent error in installing R package

I want to install NNLM ...
0
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0answers
53 views

Cell Ranger) Error during performing a test run

I am interested in the analysis of single-cell RNA-sequencing data. I installed Cell Ranger according to the instruction (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/...
1
vote
2answers
747 views

bcl2fastq2 v2.20.0 converstion software on Ubuntu 18.04

bcl2fastq is a program that converts Illumina run output from .bcl to fastq. I'm having difficulties installing the software I downloaded from Illumina on my Ubuntu 18.04. I've followed their ...
0
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1answer
45 views

Repeatscout installation problem

I've installed Repeatscout from https://bix.ucsd.edu/repeatscout/. I've also installed TRF and nseg required by the program. I followed the steps: ...
0
votes
1answer
91 views

UCSC packages/tools ucsc-netchainsubset and ucsc-fatotwobit not working on GNU/Linux

I have installed some ucsc tools on my Mac computer and it worked fine: Installation ...
2
votes
2answers
888 views

How to use busco installed through conda?

I have installed busco on my Mac computer using conda install --channel bioconda busco=3.0.2 into an environment called ...
2
votes
2answers
387 views

Unable to install bedtools on windows 10 ubuntu

I am trying to install bedtools on windows 10, but I get an error I don't understand. How can I fix it? ...
2
votes
1answer
96 views

Why can I not install snakemake on my SLURM computer even though I can find it in the bioconda channel?

I searched for the package 'snakemake' on my SLURM cluster using: conda search --channel bioconda snakemake and I get many versions, up to 5.4.2. I then try to ...
1
vote
0answers
45 views

failed to install hdf5r [duplicate]

I failed to install hdf5r using this command provided by https://satijalab.org/seurat/mca_loom.html: devtools::install_github(repo = 'hhoeflin/hdf5r'),below is the code,can you help me ?
0
votes
1answer
636 views

R studio failed to install the latest development version of hdf5r from Github (win10)

I install hdf5r following https://github.com/hhoeflin/hdf5r, it shows two methods: When I use the second method to install from github,it showed many errors: ...
2
votes
1answer
194 views

Error in PSI-BLAST when running psipred locally

I am very new to bioinformatics and Linux and am trying to run psipred locally on Ubuntu 18.04 but cannot get PSI-BLAST to work. I have downloaded BLAST legacy version 2.2.26 and unpacked it, uniref90 ...
3
votes
2answers
905 views

Installing DESeq2 in Ubuntu

I am trying to install DESeq2 in my Ubuntu with R version 3.5.1. According to the package repository in Bioconductor the version should be 3.5. ...
1
vote
1answer
101 views

Error compiling HMMER v3.2.1

I tried to compile HMMER v3.2.1 in Cygwin using ./configure followed by make or ...
2
votes
1answer
68 views

hgsql not found when running a script despite being accessible on command-line

I am working on macOS. I am following the steps described here to lift over an annotation from the reference genome of C. elegans to another assembly of C. elegans. I have run this code: ...
0
votes
1answer
934 views

How to uninstall hmmpress from my conda environment?

I have installed hmmpress on my Mac OS X. It is here: which hmmpress /Users/user/anaconda/bin/hmmpress It is available in my ...
4
votes
1answer
339 views

Psipred installation

I am trying to install psipred in a unix server. Psipred is installed, but fails because it can not find the correct database files. I have downloaded uniprod90.fasta. Psipred also loads the old ...
0
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1answer
205 views
3
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1answer
57 views

TRAL does not find “Phobos result file”

I want to use TRAL to annotate tandem repeats in the reference genome of Caenorhabditis elegans. For this, I need to install some external software, such as Phobos. I've downloaded Phobos and I am ...
5
votes
4answers
1k views

tRNAscan-SE error: FATAL: Unable to find /usr/local/bin/cmsearch executable

I have downloaded tRNAscan-SE from here. After decompressing and untaring the file, I installed it using: ./configure make make install When I type ...
4
votes
1answer
101 views

Problem installing last build of Sniffles

I have followed the steps described here to install Sniffles on my Mac Book Pro running macOS High Sierra. However, I am struggling with this step: ...
1
vote
1answer
40 views

Installing Rostlab's PredictProtein

I am trying to install Rostlab's PredictProtein in a Virtual Machine as detailed here https://rostlab.org/owiki/index.php/How_to_Run_The_PredictProtein_Machine_Image_with_VirtualBox: Download ...
0
votes
1answer
104 views

Create galaxy local toolshed using Planemo

I tried to create galaxy local toolshed using planemo. I used command as follows, create virtual env virtualenv .venv; .venv/bin/activate Install planemo ...
2
votes
1answer
827 views

Albacore wheel not supported on this platform (Mac OS X El Capitan)

I download the Albacore wheel from Oxford Nanopore. I activated my conda environment that has Python 3 as the default python version. I tried to install Albacore with ...
3
votes
1answer
549 views

Does MinKNOW work with Mac OSX high sierra 10.13.1?

I have done a compatibility check as described here on my computer to know if I can use MinKNOW on my mac laptop. It says that my OS is incompatible and that the OSX must be Yosemite or El Capitan. ...
2
votes
1answer
78 views

Problem installing RATT

I have followed the steps here to install RATT, i.e.: svn co "https://svn.code.sf.net/p/ratt/code/" ratt-code However, when I check my installation by running '$...
0
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3answers
235 views

How to install blasr on Mac OS X?

I am trying to install blasr on mac osx. I followed the steps here I get the error below after using the 'make' command: ...
0
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0answers
91 views

How to install and use pbhoney on Mac OSX?

I download the PBSuite from SourceForge. I decompressed the file. I then moved to this directory: PBSuite_15.8.24/pbsuite/honey and typed: ...
3
votes
2answers
419 views

RcppArmadillo installation error

When I am trying to install the RcppArmadillo Bioconductor library in R, it is giving me the following error: ...
4
votes
1answer
69 views

Cannot install chromosomer

I am trying to install chromosomer but I fail. Can anybody help me, please? ...
3
votes
0answers
928 views

How to install DnaSP on a Mac

I need to install DnaSp, but its not working on my mac. I'm using wine to install it using these instructions for wine. it successfully installs but then I get this error ...