Questions tagged [software-installation]
The software-installation tag has no usage guidance.
48
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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 ...
CommunityBot
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2
votes
1
answer
18
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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/...
- 151
2
votes
1
answer
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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
...
2
votes
1
answer
91
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arm64 installation of AMRFinderPlus
I was trying to install NCBI AMRFinderPLUS on my Nvidia Jetson using standard Bioconda based installtion. However, all the time it is giving error that the package is not available and I thought I am ...
M__♦
- 12.8k
1
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0
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What versions of pip and python are appropriate for nsdpy?
I am currently trying to download all the requirements to make a COInr database, following this workflow; https://mkcoinr.readthedocs.io/en/latest/content/overview.html.
It requires a couple different ...
- 4,212
2
votes
2
answers
77
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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 ...
- 21
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vote
1
answer
293
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ProteinPromt installation
i dont know how to build/pull this container (https://codebase.helmholtz.cloud/proteinprompt/ProteinPrompt) can you advice me how to install it?
EDIT:
My soft - Ubuntu 20.04 lts
Thanks to @M__ I ...
M__♦
- 12.8k
1
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3
answers
249
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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-...
- 1
5
votes
2
answers
546
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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.
...
- 175
2
votes
1
answer
585
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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:
...
- 1,305
2
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0
answers
29
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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 ...
M__♦
- 12.8k
2
votes
1
answer
49
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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.
...
0
votes
1
answer
3k
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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/...
CommunityBot
- 1
0
votes
2
answers
792
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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 ...
0
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0
answers
48
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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 ...
- 2,464
1
vote
0
answers
450
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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 ...
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2
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0
answers
188
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Finding bioperl on cpanmetadb failed
I failed to install bioperl on debian in the following way:
...
- 841
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1
answer
287
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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.
...
CommunityBot
- 1
0
votes
2
answers
669
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1
vote
1
answer
110
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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 ...
CommunityBot
- 1
2
votes
2
answers
114
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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 ...
- 14.9k
2
votes
1
answer
512
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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 ...
2
votes
1
answer
472
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`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 ...
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1
answer
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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 ...
M__♦
- 12.8k
1
vote
2
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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 ...
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4
votes
1
answer
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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 ...
CommunityBot
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3
votes
2
answers
2k
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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 ...
- 5,632
2
votes
1
answer
154
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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:
...
- 4,212
0
votes
1
answer
95
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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:
...
- 5,090
0
votes
1
answer
228
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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
...
- 2,479
3
votes
2
answers
1k
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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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votes
1
answer
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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：
...
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votes
1
answer
154
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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 ...
- 2,479
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0
answers
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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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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.
...
- 645
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1
answer
253
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Error compiling HMMER v3.2.1
I tried to compile HMMER v3.2.1 in Cygwin using
./configure
followed by
make
or
...
- 130
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vote
1
answer
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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 ...
CommunityBot
- 1
5
votes
4
answers
2k
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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 ...
- 2,584
1
vote
1
answer
148
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
...
CommunityBot
- 1
3
votes
1
answer
75
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 ...
- 146
0
votes
1
answer
293
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GMAJ error: Exception in thread "main" java.lang.ClassCastException: java.lang.StringBuffer cannot be cast to java.lang.String
I have installed GMAJ using:
...
- 1,576
4
votes
1
answer
180
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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:
...
- 2,479
1
vote
1
answer
49
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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 ...
- 10.5k
3
votes
1
answer
947
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. ...
- 4,723
2
votes
1
answer
108
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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 '$...
- 4,723
1
vote
3
answers
303
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:
...
- 1,816
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votes
2
answers
1k
views
RcppArmadillo installation error
When I am trying to install the RcppArmadillo Bioconductor library in R, it is giving me the following error:
...
- 4,895
4
votes
1
answer
94
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Cannot install chromosomer
I am trying to install chromosomer but I fail. Can anybody help me, please?
...
- 10.5k