Tag: bioconda

Solving environment: failed with initial frozen solve. Retrying with flexible solve. PackagesNotFoundError: The following packages are not available from current channels: 1 I am trying to install samtools on my environment bioconda with this command: bioconda install samtool I get this error: Solving environment: failed with initial frozen solve. Retrying…

hisat2-align exited with value 1 1 I am a beginner with command and bioinformatics I am trying to alignment with HISAT2 for RNA seq so first I install the HISTA2 by bioconda using this command: bioconda -c install hisat2 after that i made index for my reference genome with this…

I have this wrappers in my snakemake file rule fastqc: input: “reads/{sample}_trimmed.fq.gz” output: html=”qc/fastqc/{sample}.html”, zip=”qc/fastqc/{sample}_fastqc.zip” # the suffix _fastqc.zip is necessary for multiqc to find the file params: extra = “–quiet” log: “logs/fastqc/{sample}.log” threads: config[“resources”][“fastqc”][“cpu”] conda: “envs/qc.yaml” wrapper: “v1.31.1/bio/fastqc” qc.yaml: name: qc channels: – bioconda dependencies: – python – fastqc…

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I have problem with installing qiime2-2023.2 with conda on a server running linux system. I ran command conda env create -n qiime-2023.2 –file qiime2-2023.2-py38-linux-conda.yml. But it turned out to report the error info ERROR conda.core.link:_execute(952): An error occurred while installing package ‘bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0’.,and below for the detailed error info. At first…

NanoSim Error “Please specify the training reads and its reference genome!” 1 Hi, I installed nanosim using conda install -c bioconda nanosim and then tried to run the read characterization using read_analysis.py transcriptome -i training_reads.fastq -r reference_genome.fa -rt reference_transcriptome.fa -annot reference_annotation.gtf -o training. However, I get the following error: Please…

I have a self-hosted Nexus server running on AWSVersion Sonatype Nexus RepositoryOSS 3.54.1-01 I currently have Conda set up (as a proxy) and I would like to add 2 additional channels to this conda proxy – bioconda and conda-forge I am having trouble with the configuration for this – do…

Oddant1 (Oddant1) May 23, 2023, 5:52pm 3 Hello @PatoUru, can you post the content of your .condarc file here? There could be some channel overrides in there causing this issue. Another potential cause is an overly aggressive firewall particularly if you are attempting to install on a system behind an…

I was using R in RStudio under a conda environment with various bioconductor packages. But suddenly I ran into this error when I tried to load a package: ImportError: /home/user/anaconda3/envs/dmcgb/bin/../lib/libstdc++.so.6: version `GLIBCXX_3.4.30′ not found (required by /lib/x86_64-linux-gnu/libLLVM-13.so.1) It is not the first time that I have this error so I…

Hello!I tried to install qiime2-2023.2 with miniconda3 under Windows Subsystem for Linux but met error message.The error message was below.ERROR conda.core.link:_execute(740): An error occurred while installing package ‘bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0’.Rolling back transaction: doneclass: LinkErrormessage:post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0location of failed script: /home/elaine/miniconda3/envs/qiime2-2023.2/bin/.bioconductor-genomeinfodbdata-post-link.sh==> script messages <== ==> script output <==stdout:stderr: QIIME is…

How can I update fastq-dump to 3.0.0? 2 Hello! I’m trying to install the latest version of fastq dump, but all I could achieve is to install the 2.8.0, even though I used the code that is written on the Sra tools website (anaconda.org/bioconda/sra-tools). I want to install at least…

emst7885 (Emelie) May 12, 2023, 12:32pm 1 Dear QIIME2 Team! I want to use Rescript to reverse transcribe rna-sequences (from Silva) to dna sequences. I have just upgraded to the latest version of QIIME2 (2023.2) installed via conda in a new environment. Thereafter I installed Rescript in my activated QIIME2-2023.2…

MULTIQC problem 1 I’m trying to install multiqc on my Ubuntu virtual machine but I get some errors I do these steps 1- I activate my environment then I do this command conda install -c bioconda multiqc then i try to do multiqc by this command multiqc + my fastq…

tophat2 installation error 1 Hi, I am trying to install tophat2 . tried this command conda install -c bioinfo tophat2 but got this error : Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): done Solving environment: failed with…

Research software is like the tower-building game Jenga — tools atop tools atop tools. When developers tweak their individual pieces, this can change the function of the software that depends on them, potentially altering results — or causing the software to fail. Version 3.6.0 of the R programming language, for…

Hello, I’m currently following this paper Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation. It is a ChIP-Seq to generate genome-wide maps of 34 chromatin modifications (17 acetylation marks, and 17 methylation marks) and the histone variant H2AZ. B cells were either naïve (G0) or activated for…

I am trying to run a snakemake pipeline with packages installed from a main.yml file. One of the dependencies of the package is samtools, Previously, having the dependency listed as samtools did not seem to run into any problems. The actual yml file is: name: yevo_pipeline_env channels: – defaults -…

  pbfusion is a new software tool for detecting gene fusions and other transcriptional abnormalities in PacBio Iso-Seq data. The advancement of cancer research depends on the ability to accurately detect the molecular changes driving the initiation, progression, and evolution of tumors. In particular, gene fusions can lead to transcriptional…

dnfarsi (Dominic Farsi) April 10, 2023, 11:14am 1 Hello I appear to be having a similar issue. However I don’t have the (core dumped). I am using Ubuntu 22.04 LTS and installed miniconda and then natively installed qiime2. When using any qiime command I get this illegal instruction. Interestingly it…

HiI used qiime 1 extensively. Moved away for a while.I’m trying to install qiime 2 using miniconda using$ wget data.qiime2.org/distro/core/qiime2-2023.2-py38-linux-conda.yml This runs good.Next, when I tried to create environment using .. $ conda env create -n qiime2-2023.2 –file qiime2-2023.2-py38-linux-conda.yml Collecting package metadata (repodata.json): doneSolving environment: failed ResolvePackageNotFound: q2-vsearch=2023.2.0 sepp=4.3.10 q2-diversity-lib=2023.2.0…

Problem with fatsq-dump 0 Hi, I am absolutely new in NGS data analysis and have just started working in centos. I installed sratoolkit with the commands : conda create –n sratoolkit_env –y conda activate sratoolkit_env conda install –c bioconda sra-tools –y Then as given in the Biostar Handbook (Bioinformatics Data…

I’m attempting to create a python GUI for analysing tRNA-Seq data that can run on Linux and Windows. It is necessary to run several applications, such as bowtie2, samtools, or bedtools, which can be readily downloaded by anaconda on Linux but is a pain on Windows. Because these apps cannot…

Hi!I am a first-time doer of bioinformatics (and recovering luddite), attempting to use the q2 galaxy interface for my workflow.I’m following this tutorial for setting everything up with docker: Running QIIME 2 inside Galaxy (alpha release version) – YouTube.It was going well until I went to upload the atacama metadata…

cdiener (Christian Diener) March 2, 2023, 7:31pm 1 Hi, I noticed that the CI for our Qiime2 plugin is failing for older versions now. In particular newer versions of conda don’t seem to be able to install the environment for Qiime2 2022.8: Run wget raw.githubusercontent.com/qiime2/environment-files/master/2022.8/release/qiime2-2022.8-py38-linux-conda.yml –2023-03-02 19:16:39– raw.githubusercontent.com/qiime2/environment-files/master/2022.8/release/qiime2-2022.8-py38-linux-conda.yml Resolving raw.githubusercontent.com…

I have a nextflow workflow for which I am running with sge + apptainer profile using the command nextflow run main.nf -profile sge,apptainer but I am receiving the error line #: bwa: command not found I have tried running apptainer run workflow.sif to check, and bwa as well as other…

Conda is installing older version of Spades even though latest version is there in the bioconda repository 1 I am trying to install spades using conda. Even though the bioconda has the latest version, the version getting installed in my system is an older version 3.13. Initially, I thought creating…

My suggestion is to run prokka from within conda by simply downloading miniconda then conda create –name prokka conda activate prokka conda install -c conda-forge -c bioconda -c defaults prokka prokka –help prokka –version prokka mycontigs.fa # running prokka You could always perform a chmod 700 /home/saurab/BIOIN/phastest-app/sub_programs/barrnap or some variant…

Hi all, I’m trying to create a conda environment through a .yml file that has all the required dependencies for a certain project but I run into environment conflicts. I figured out the source of this conflict, which stems from two specific dependencies, but for some reason, creating an environment…

Hi all. I’m trying to use songbird as a plugin for qiime2. I’ve tried first installing it with qiime2-2022.11 (the latest version) because it seems to be a plugin now. But I kept running into an error regarding tensorflow version when I used conda install:conda install -c conda-forge -c bioconda…

samtools missin 0 Hello, I just had a fresh galaxy installation. however, the correct barcodes tool from ‘dunovo’ package seems to have an issue with samtools being missing. I just dont understand why samtools are not already part of the tool dependencies, hence galaxy would install them automatically once i…

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…

How to create Dockerfile without copying large data input and Build image such that snakemake wokflow run as Entrypoint 1 I have project folder structure like Below : which has size of more than 50 GB . When i am creating Dockerfile such that Snakefile workflow which utilizes data from…

Containers are a technology for packaging and deploying software applications in a portable and isolated environment. They allow developers to bundle their application and its dependencies together in a single package, called a container. This package can then be run on any machine that has a container runtime, such as…

turtle February 6, 2023, 5:30pm 1 Sorry for posting the same problem again.I’m having ALDEx2 plugin error. I tried the following code, conda install bioconductor-aldex2 -c defaults -c bioconda -c conda-forge conda install -c dgiguere q2-aldex2 But the error showing is, I was able to install ALDEx2 in R but…

ivanllam (Ivan Lam) February 2, 2023, 4:29am 1 Hi all, I aim to install QIIME2-2022.11 on Mac. I encounter the following error similar to (Error to install qiime2-2022.2 with conda). The recommendation involve a Mac with a M1 chip, but my Mac is working with a Intel Core-i9. May I…

Mugsy not working 0 hello, I have installed mugsy using bioconda and it was installed without any error. Now I can see mugsy in my enviroment but whenever I do source activate mugsy it says “-bash: activate: No such file or directory”, but when I do conda activate mugsy, it…

setting up Kallisto software 1 Hi, I have tried to set up Kallisto software – following the instructions on protocols.hostmicrobe.org/conda without any luck. I need this software to align reads to a reference genome for RNA sequencing analysis. It worked up until I used the command: conda create –name rnaseq…

Tutorial:Analysis of Smart-Seq3 data with kallisto-bustools 0 Based on @dsull’s answer. The smart-seq3 analysis is handled by the kallisto-bustools pipeline. Create a conda environment if needed. Create the conda environment file and save it as env_kb.yml. # conda environment for kallisto bustools pipeline name: kb channels: – bioconda – conda-forge…

Only very recently (~2 weeks ago), cutadapt installed via conda has the following error: This is cutadapt 3.2 with Python 3.8.6 Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC in2438_3_CKDL210000739-2a-AK5142-AK6697_HVHF2DSXY_L2_1.fq.gz Processing reads on 4 cores in single-end mode … [———>8 ] 00:00:26 5,536,084 reads @…

Using genelab-utils to download GeneLab workflows – HackMD — tags: GeneLab title: Using genelab-utils to download GeneLab workflows — # Using genelab-utils to download GeneLab workflows > New download program added (as of v1.1.03) for downloading GeneLab workflows based on our plan on releasing assets with a zip of specific…

Here’s my command:conda env create -n test-qiime2_env -f qiime2-2022.11-py38-linux-conda.yml 2> qiime2-2022.11-py38-linux-conda.yml.e 1> qiime2-2022.11-py38-linux-conda.yml.o Here’s my log files: (base) cat qiime2-2022.11-py38-linux-conda.yml.o Collecting package metadata (repodata.json): …working… done Solving environment: …working… done Preparing transaction: …working… done Verifying transaction: …working… done Executing transaction: …working… done Rolling back transaction: …working… done (base) cat qiime2-2022.11-py38-linux-conda.yml.e…

Are package downgrades a necessary evil in Conda? 1 I am just trying to get my head around using conda environments. I created a conda environment for a project containing plink2, plink, R and bcftools. When I installed plink, using mamba install -n autozygosity -c conda-forge plink, I got the…

Building a Simulated Metagenomic Dataset – HackMD       Published Linked with GitHub — tags: ‘JPL: Genetic Inventory Project’ — # Building a Simulated Metagenomic Dataset Here we’ll create a simulated metagenomic datasets for controlled testing. This dataset was used to determine the Kraken 2 confidence score that best…

I’m trying to install the Bioconductor package liftOver using conda. I’m creating a conda environment using a .yml file like this: conda env create -f coo_environment.yml When I do this, I get: Collecting package metadata: done Solving environment: failed ResolvePackageNotFound: – bioconductor-liftover The relevant contents of coo_environment.yml are shown below…

Installing ensembl-vep 1 Hello all , I tried installing ensembl-Vep on mu ubuntu using following commands git clone github.com/Ensembl/ensembl-vep cd ensembl-vep perl INSTALL.pl I got the error as :- ERROR: DBI module not found. VEP requires the DBI perl module to function I tried installing DBI etc but the error…

Mapping reads using kallisto – rna seq analysis 0 Hi, I’m trying to map reads to a reference genome using kallisto for rna seq analysis with terminal on mac and the following command keeps loading for hours and won’t run. I’m not exactly sure where I’ve gone wrong. kallisto index…

Hello,I am opening an issue here for a problem that I don’t think you guys can solve, but you never know. I recently developped a Python tool, and I need to get it onto the Bioconda repository . To do this, I have created a recipe that I must know…

From your command line it appears you are on windows. There are several veresions of pybedtools on bioconda, however, if I grep through them, they are all for the linux platform. If you’re on Windows 10, you could consider setting up the ‘windows subsystem for linux’ (and possibly Xming), installing…

I’m a relatively new qiime2 (bioinformatics tool based on python language) and python user. So far, I have been using qiime2 inside a virtual machine, which is ok but not great. Since I’m taking a python course and have gotten used to work with pycharm, I’m trying to install the…

Conda recipes for the bioconda channel. 4571 Projects Similar to Bioconda Recipes Sequenceserver Intuitive local web frontend for the BLAST bioinformatics tool Homebrew Bio 🍺🔬 Bioinformatics formulae for the Homebrew package manager (macOS and Linux) Galaxy Data intensive science for everyone. Travel Guide “A travel guide to suggest activities you…

Explore SNVs associations with traits of UK BioBank. GWAS study results where made publicly available courtesy of Neale’s Lab on August 1st, 2018. For more information please visit: www.nealelab.is/uk-biobank INSTALL In R: devtools::install_github(“adRn-s/ukbbgwas”). DEV(s) Dependencies Mandatory and optional dependencies can all be handled with bioconda. Here’s a complete YAML specification…

conda 252.4 kB | linux-64/ultraplex-1.2.5-py37h8902056_1.tar.bz2  1 month and 7 days ago bioconda 14 main conda 255.2 kB | linux-64/ultraplex-1.2.5-py39hbf8eff0_1.tar.bz2  1 month and 7 days ago bioconda 27 main conda 256.2 kB | linux-64/ultraplex-1.2.5-py38hbff2b2d_1.tar.bz2  1 month and 7 days ago bioconda 16 main conda 240.1 kB | osx-64/ultraplex-1.2.5-py37h8dbb1ac_1.tar.bz2  1 month and…

I’m trying to install busco, detonate, and transrate in conda but I keep getting this error: The environment is inconsistent, please check the package plan carefully The following packages are causing the inconsistency: – bioconda/linux-64::samtools==1.11=h6270b1f_0 – bioconda/linux-64::trinity==2.9.1=h8b12597_0 This is the command I enter conda install -c bioconda busco -y So…

Using a Mac with M1 chip, I’m trying to install the following Bioconda packages: cutadapttrim-galoresamtoolsbedtools.htseq.bowtie2.deeptools.macs2 I’ve been able to install picard and fastqc with no issues, but all others turn out one of two error messages: PackagesNotFoundError: The following packages are not available from current channels: or Found conflicts! Looking…

conda samtools 0 It gives me error when installing samtools I installed curl -O repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh sh Miniconda3-latest-MacOSX-x86_64.sh conda install -c bioconda samtools zsh: command not found: conda javierpalomares@JAVIERs-Air ~ % samtools conda • 184 views Login before adding your answer. Read more here: Source link

I was given some code of a previous intern and I’m supposed to find out what it does. It is a snakemake pipeline that has a my_pipeline.yaml file which is supposed to contain all the ‘general packages needed for the pipeline’ The file looks like this: name: my_pipeline channels: -…

I am using the conda env of faststructure from bioconda channel. Got this error messages. Could it be that the bioconda package needs to be updated? Best regards: python structure.py structure.py:3: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 import fastStructure structure.py:4: RuntimeWarning: numpy.dtype size changed,…

The true power of the state space model is to allow the creation and estimation of custom models.This notebook shows various statespace models that subclass sm. That means your MAGeCK python module is installed in /home/john/.pyenv/versions/2.7.13/lib/python2.7/sitepackages.I use conda to install the latest version of. This twovolume set Diseases and Pathology…

Conda is a platform- and language-independent package manager that sports easy distribution, installation and version management of software. The bioconda channel is a Conda channel providing bioinformatics related packages for Linux and Mac OS. This repository hosts the corresponding recipes. User guide Please visit bioconda.github.io for details. Developer guide Please…

conda channels what is conda channels ? Conda channels are the locations where packages are stored. They serve as the base for hosting and managing packages. Conda packages are downloaded from remote channels, which are URLs to directories containing conda packages set up channels The conda-forge channel contains many general-purpose…

About Short intro Further reading How to cite Brief project history Authors Funding License and Terms of use Short intro QUAST evaluates genome assemblies by computing various metrics, including N50, length for which the collection of all contigs of that length or longer covers at least 50% of assembly length…

rust-bio-tools-0.35.0 is not a library. A set of ultra fast and robust command line utilities for bioinformatics tasks based on Rust-Bio. Rust-Bio-Tools provides a command rbt, which currently supports the following operations: a linear time implementation for fuzzy matching of two vcf/bcf files (rbt vcf-match) a vcf/bcf to txt converter,…

I’m trying to install VEP in a conda environment, but it keeps failing. I’ve tried with the normal installation process: conda install -c bioconda ensembl-vep But get the below errors which run for about an hour and eventually fail: $ conda install -c bioconda ensembl-vep Collecting package metadata (current_repodata.json): done…

Conda failing to install VEP 0 I’m trying to install VEP in a conda environment, but it keeps failing. I’ve tried with the normal installation process: conda install -c bioconda ensembl-vep But get the below errors which run for about an hour and eventually fail: $ conda install -c bioconda…

I’ve tried using the standard alphafold2 setup via docker (converted to a singularity container) via the setup described at github.com/kalininalab/alphafold_non_docker, and both result in the following error: […] E1210 12:01:01.009660 22603932526400 hhblits.py:141] – 11:49:18.512 INFO: Iteration 1 E1210 12:01:01.009703 22603932526400 hhblits.py:141] – 11:49:19.070 INFO: Prefiltering database E1210 12:01:01.009746 22603932526400 hhblits.py:141]…

I’m going to use the comment posted by @cboettig in order to resolve this question. Packrat Packrat is a dependency management system for R. Gives you three important advantages (all of them focused in your portability needs) Isolated : Installing a new or updated package for one project won’t break…

TLDR: Thanks to funding from EOSC-Life, the Freiburg Galaxy team will work in 2022 with Biolytix, a Swiss Small and Medium-sized Enterprise (SME) specialized in molecular biology and microbiological analyses, toward Accessible and scalable detection and identification of foodborne pathogens. Background Food contaminations with pathogens are a major burden on…

Listing Results Biopython Contact Us Biopython · Biopython 2 hours ago Biopython.org View All Biopython. See also our News feed and Twitter. Introduction. Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.. It is a distributed collaborative effort to…

Listing Results Biopython Contact Map Protein Contact Maps using Biopython Warwick 9 hours ago Warwick.ac.uk View All Protein Contact Maps using Biopython. When working with protein 3D structures, a contact map is usually defined as a binary matrix with the rows and columns representing the residues of two different chains….

AlphaFold This package provides an implementation of the inference pipeline of AlphaFold v2.0. This is a completely new model that was entered in CASP14 and published in Nature. For simplicity, we refer to this model as AlphaFold throughout the rest of this document. Any publication that discloses findings arising from…

Align fastq SOLiD data 1 Hello everyone, I have downloaded some data from the short read archive using the sratoolkit. The data is SOLiD data. I have seen people using the Lifescope (Life Technologies) to align the reads, as I presume it works for this type of data. But unfortunately,…

Forum:Kmergenie module readfq not found 0 I have been trying to run kmergenie for my data on ubuntu and every time I enter the code it gives an import error: no module named readfq. I have tried downloading the module from bioconda and when checking the directory it showed that…

As a novice to this community (and technology) I have only a basic knowledge regarding how to build and deploy a docker so i was hoping someone could provide some help. The situation is the following: I wanna create a docker container with two conda environments and I wanna call…

How to install hisat2 on Mac OS Big Sur 0 I’d like to install HISAT2 on Mac OS Big Sur ver.11.5.2. I have tried to install HISAT2 by using bioconda (Hisate2 :: Anaconda), and the installation seemed to be successful, but when I tried to start hisat2, I’m getting the…

snpeff : wont recognize the gtf or gff3 files (runtime exception) 1 Hi, I am trying to build a custom databasee for snpeff. As instructed both in the forum and snpeff instructions, I did the following; Then I added the following into snpEff.config file # BG94_1 BG94_1.genome : BG94_1 Then…

Are there any alternatives to Liftoff – Mapping annotations (GFF/GTF) between assemblies 2 Hi, I am annotating closely related accession (varieties) using reference assembly (please note that I am using only a region, so that is the reason why you don’t see chromosome info). I really liked liftoff (ver 1.6.1:…

Request for the process about install ‘fastANI’ on MacOS 0 When I use the below scripts to install the software ‘fastANI’ on my MacBook, there were a series of problems. I am not so good at the bioinformatics, and I want to know how to install this software on the…

Get chromosome sizes from fasta file 4 Hello, I’m wondering whether there is a program that could calculate chromosome sizes from any fasta file? The idea is to generate a tab file like the one expected in bedtools genomecov for example. I know there’s the fetchChromSize program from UCSC, but…

Pybedtools error sans 20-08-2021 pysam – Error when I install samtools for python on windows – i trying install pysam, pybedtools modules on python got error: ($i=1; $i[email protected] temp]$ conda install pysam bedtools hisat2 [ snip. However,…

Tutorial for de-novo repeat library construction The RepeatMasker software includes a lot repeat library. You can query them using: queryTaxonomyDatabase.pl -h queryRepeatDatabase.pl -h If there is no repeat library available for your species, you may want to create your own.Prerequisite Lot of time (the repeatmodeler and transposonPSI steps can run…

If you are on a Mac then this is not the right executable. You will need to download Mac executable from here: hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/ You may still run in to library errors if you are using latest BigSur OS. Your best bet is to use conda to install. conda install -c…