Questions tagged [software-installation]
The software-installation tag has no usage guidance.
48 questions
2
votes
1
answer
116
views
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 ...
- 43
1
vote
0
answers
53
views
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 ...
Grace Sheehan
1
vote
1
answer
323
views
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 ...
- 147
5
votes
2
answers
573
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.
...
- 51
1
vote
3
answers
276
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-...
- 211
2
votes
1
answer
596
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:
...
- 149
2
votes
0
answers
31
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 ...
- 381
2
votes
1
answer
50
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.
...
- 23
2
votes
1
answer
18
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/...
- 21
0
votes
0
answers
49
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
213
views
Finding bioperl on cpanmetadb failed
I failed to install bioperl on debian in the following way:
...
- 463
1
vote
0
answers
469
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
117
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 ...
- 21
2
votes
1
answer
481
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
299
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.
...
- 203
2
votes
2
answers
80
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 ...
- 2,479
0
votes
2
answers
834
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 ...
- 177
1
vote
1
answer
111
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 ...
- 11
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 ...
- 13
0
votes
2
answers
683
views
0
votes
1
answer
3k
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/...
- 87
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
99
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:
...
- 171
0
votes
1
answer
235
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
...
- 2,479
3
votes
2
answers
3k
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 ...
- 2,479
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?
...
- 41
3
votes
1
answer
154
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 ...
- 2,479
1
vote
0
answers
58
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 ?
- 39
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
525
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 ...
- 21
4
votes
2
answers
3k
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.
...
- 645
1
vote
1
answer
260
views
Error compiling HMMER v3.2.1
I tried to compile HMMER v3.2.1 in Cygwin using
./configure
followed by
make
or
...
- 11
2
votes
1
answer
155
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:
...
- 2,479
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 ...
- 2,479
4
votes
1
answer
693
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 ...
- 645
0
votes
1
answer
293
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:
...
- 2,479
3
votes
1
answer
77
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 ...
- 2,479
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 ...
- 2,479
4
votes
1
answer
180
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:
...
- 2,479
1
vote
1
answer
50
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 ...
- 113
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
...
2
votes
1
answer
1k
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
...
- 2,479
3
votes
1
answer
953
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. ...
- 2,479
2
votes
1
answer
108
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 '$...
- 2,479
1
vote
3
answers
307
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:
...
- 2,479
3
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:
...
- 2,578
4
votes
1
answer
95
views
Cannot install chromosomer
I am trying to install chromosomer but I fail. Can anybody help me, please?
...
- 2,479
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 ...