Questions tagged [software-installation]

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2 answers
88 views

Error installing VEP on mac

I have tried multiple different ways to get Ensemble's Variant Effect Predictor (VEP) to properly install on my mac, but I keep getting same error. ...
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1 vote
2 answers
49 views

How do I install shapeit4 on Ubuntu/Mint?

I'm having trouble install shapeit4 4.2.2 on my new Mint 21 installation (Ubuntu 22.04 LTS). According to the official docs, the requirements are: HTSlib: A great C library for reading/writing high-...
2 votes
1 answer
110 views

Struggling to install scvi-tools on Mac M1

I was wondering if somebody here has experience with installing scvi-tools on a Mac with M1 chip. I tried the following command: ...
2 votes
0 answers
21 views

Building database for MetaCache takes extremely long

A question to those who have experience with MetaCache (metagenomic tool): I have tried to build the MetaCache taxonomy from refseq (only bacteria), as described in the EXAMPLES here. However, the ...
2 votes
1 answer
41 views

the following errors are found during the installation of an open source software, UNCeqR on z shell

I am trying to do somatic mutation detection via the open source software, UNCeqR I got following error was detected on mac z shell during installation. ...
1 vote
0 answers
8 views

Issue with iCTNet2 installation

Has anyone encountered this same installation issue of iCTNet2? I encountered this issue for installation of iCTNet2 via Cytoscape App Manager and similarly via installation from website download/...
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0 votes
0 answers
39 views

install a CRAN package that imports a CRAN package that imports a Bioconductor package

I have a CRAN package say myPack, that imports two CRAN packages, say cranA and cranB. These ...
2 votes
0 answers
32 views

Finding bioperl on cpanmetadb failed

I failed to install bioperl on debian in the following way: ...
1 vote
0 answers
189 views

tmhmm installation and running

I am trying to predict transmembrane protein using tmhmm-2.0c. According to Package instruction, I have changed the path of perl inside the program like as ...
2 votes
2 answers
80 views

How do I install hammock?

I'm working with phage peptides libraries. Currently I'm analysing a massive data set from phage selection, NGS readout, preprocessed already (fasta file). I want to analyse the sequences to cluster ...
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2 votes
1 answer
298 views

`TxDb.Hsapiens.UCSC.hg19.knownGene` and `EnsDb.Hsapiens.v75` can't be installed

I think there is a problem with TxDb.Hsapiens.UCSC.hg19.knownGene and EnsDb.Hsapiens.v75. I'm struggling to install all of ...
  • 175
0 votes
1 answer
186 views

install bowtie2 from sources cannot find -ltbb

I am trying to install bowtie2 aligner from sources without the root access. Bowtie2 needs tbb package to be installed and it is recommended to install oneTBB. ...
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2 votes
1 answer
40 views

How can I run the fdnadist command from the EMBOSS package?

My operating system is Mac OS X. I would like to compute DNA distances between different sequences. For this, the dnadist package from the Phylip software would be good but hard to automate. EMBOSS ...
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0 votes
2 answers
555 views

Installing HiC-Pro issues

I am setting up a HiChIPseq pipeline, but installing software necessary for the HiC side of things has been unbecoming. Both my PI and I have tried to install Hi-C Pro onto our Mac Pro that we use as ...
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1 vote
1 answer
100 views

Master of Pores Installation Mac OS Mojave 10.14

I'm bit of a newbie with ONT analyses and am having some trouble with the Master Of Pores installation instructions (https://biocorecrg.github.io/master_of_pores/install.html). I've managed to install ...
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1 vote
1 answer
2k 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 ...
0 votes
2 answers
530 views

Permanent error in installing R package

I want to install NNLM ...
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0 votes
1 answer
2k 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/...
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1 vote
2 answers
3k 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 ...
  • 361
0 votes
1 answer
77 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: ...
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0 votes
1 answer
168 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 ...
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3 votes
2 answers
2k 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 ...
  • 2,429
3 votes
2 answers
1k 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? ...
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3 votes
1 answer
139 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 ...
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1 vote
0 answers
57 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 ?
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0 votes
1 answer
2k 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: ...
  • 39
2 votes
1 answer
422 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 ...
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4 votes
2 answers
2k 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. ...
  • 557
1 vote
1 answer
159 views

Error compiling HMMER v3.2.1

I tried to compile HMMER v3.2.1 in Cygwin using ./configure followed by make or ...
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2 votes
1 answer
124 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: ...
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1 vote
1 answer
1k 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 ...
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4 votes
1 answer
574 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 ...
  • 557
0 votes
1 answer
288 views

GMAJ error: Exception in thread "main" java.lang.ClassCastException: java.lang.StringBuffer cannot be cast to java.lang.String

I have installed GMAJ using: ...
  • 2,429
3 votes
1 answer
73 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 ...
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5 votes
4 answers
2k 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 ...
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4 votes
1 answer
172 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: ...
  • 2,429
1 vote
1 answer
45 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 ...
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1 vote
1 answer
140 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
1 answer
998 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 ...
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3 votes
1 answer
867 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. ...
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2 votes
1 answer
104 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 '$...
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1 vote
3 answers
269 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: ...
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3 votes
2 answers
866 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
1 answer
88 views

Cannot install chromosomer

I am trying to install chromosomer but I fail. Can anybody help me, please? ...
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5 votes
1 answer
2k views

How to install DnaSP on a Mac

I need to install DnaSp, a nice GUI originally written for Windows for the population genetics of nucleotide sequence data. However, its not working on my mac. I'm using wine to install it using these ...