Tag: bioconda

How to setup the pipeline of the RNA-Seq FASTQ file processing (macOS version)

This is a guide for preparing for importing RNA-Seq FASTQ files to Subio Platform on a Mac computer. If you use a Windows10 machine, please go to the guide for Windows10. Subio Platform utilizes the following tools to process the RNA-Seq FASTQ files. fastp to trim adapters and filter low-quality…

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installation – Issue Installing Bowtie2 and Samtools on Mac M2

I am trying to install NGS analysis packages (bowtie2, samtools, etc) into mamba environments on my Mac M2, but am facing issues. I am installing as follows: mamba activate myenv mamba install -c bioconda bowtie2 And I am getting the same error as described above: Could not solve for environment…

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Unable to install bioconda and bowtie

Unable to install bioconda and bowtie 0 ➜ ~ conda install -c “bioconda/label/cf201901” bowtie 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 initial frozen solve. Retrying with flexible solve. PackagesNotFoundError: The following packages…

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Linux: segmentation fault (core dumped)

Linux: segmentation fault (core dumped) 0 Hey everyone, When trying to download any programs using “conda install -c bioconda” I get the following error: Segmentation fault (core dumped) I am not sure what this means or how to go about fixing it. Any input is appreciated! conda miniconda3 Linux •…

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Some issue about itsxpress2 plugin in QIIME2-202309 – Community Plugin Support

ZhangSR (June) December 7, 2023, 6:36am 1 Hi~ When I updated the ITSxpress within QIIME2-202309 following the updated tutorial here github.com/USDA-ARS-GBRU/itsxpress-tutorial/blob/master/ITSxpress-tutorial.md, there were some confusions. I updated the itsxpress by conda install -c bioconda itsxpress and then qiime dev refresh-cache under the QIIME2 environment I failed to call itsxpress by…

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Can’t install hisat2 with miniconda

Can’t install hisat2 with miniconda 0 I’ve been trying to install hisat2 with Miniconda but I keep getting this error. Miniconda is updated and seemingly installed. Also I’m on Mac OS. Please Advise. Channels: bioconda default defaults conda-forge Platform: osx-arm64 Collecting package metadata (repodata.json): done Solving environment: failed PackagesNotFoundError: The…

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Fastest way to convert BED to GTF/GFF with gene_ids?

This is probably a duplicated question from: How To Convert Bed Format To Gtf? How to convert original BED file to a GTF ? Converting different annotation file formats (GTF/GFF/BED) to each other How to change scaffold.fasta file or scaffold.bed file to GTF file? Convert bed12 to GFF convert bed12…

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Head of the Medical Bioinformatics platform (m/f/d) – Kiel

Das Universitätsklinikum Schleswig-Holstein (UKSH) verbindet internationale Spitzenforschung mit interdisziplinärer Krankenversorgung. Wir sind einziger Maximalversorger und größter Arbeitgeber des Landes. Unsere mehr als 14.500 Mitarbeiter*innen stellen eine höchst individuelle Versorgung sicher – unverzichtbar für die Menschen in Schleswig-Holstein.The Institute of Clinical Molecular Biology (IKMB)The Medical Faculty together with the Institute of…

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Python Tools for Genomic Data Analysis: From Sequences to Structures | by Bao Tram Duong | Nov, 2023

Analyzing genomic data, from sequences to structures, is a critical aspect of bioinformatics. Python has a rich ecosystem of tools and libraries specifically designed for genomic data analysis. Here’s an overview of key tools and libraries for various stages of genomic data analysis: Description: Biopython is a comprehensive open-source collection…

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: error while loading shared libraries: libcrypto.so.1.0.0:

bcftools error: : error while loading shared libraries: libcrypto.so.1.0.0: 1 I’m having trouble installing bcftools using conda and mamba run the following code : conda install -c bioconda bcftools but there is Errors in the results bcftools error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such…

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HDF5 brew issue // conda installation issue

I have used kallisto in the past, but now am struggling to get bootstrapping to work on a new computer (MacBook M1). I have searched through the issues that others encountered and tried three different methods of installation, but still no luck. Could you please help or direct me to…

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picrust2 installation error on mac m2

I am trying to install Picrust2 on a mac m2 and am getting installation errors regarding incompatible packages (perhaps a type or missing channel).  Looking for: [‘picrust2=2.5.2’] bioconda/osx-arm64                                 124.0 B @ 154.0 B/s  0.8s…

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PackagesNotFoundError on conda for pytorch

I want to install Pytorch 1.12 version, the CUDA version is 11.3, the python version is 3.9.18. Using the command as the following: conda install -c conda.anaconda.org/conda-forge/ pytorch==1.12.0 torchvision==0.13.0 torchaudio==0.12.0 cudatoolkit=11.3 -c pytorch But, it reports the error: (DL) C:\Users\daiyij>conda install -c conda.anaconda.org/conda-forge/ pytorch==1.12.0 torchvision==0.13.0 torchaudio==0.12.0 cudatoolkit=11.3 -c pytorch Collecting…

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Bioconductor – Bioconductor 3.18 Released

Home Bioconductor 3.18 Released October 25, 2023 Bioconductors: We are pleased to announce Bioconductor 3.18, consisting of 2266 software packages, 429 experiment data packages, 920 annotation packages, 30 workflows and 4 books. There are 69 new software packages, 10 new data experiment packages, 8 new annotation packages, no new workflows,…

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conda – How to install Bioconda packages

The Bioconda channel builds packages with the Conda Forge channel prioritized. This requires users to likewise prioritize the Conda Forge channel when installing Bioconda packages (see Bioconda documentation). That is, the correct formulation for specifying channels at install time is: conda install -c conda-forge -c bioconda foo Global configuration and…

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SRR download using fasterq-dump

SRR download using fasterq-dump 1 Hello, I have downloaded the sra-toolkit from Anaconda (anaconda.org/bioconda/sra-tools) and downloaded an .sra file using the command: prefetch SRR20073591. The .sra file is located here: /faststorage/project/Biof/testdir/SRR20073591/SRR20073591.sra. When I navigate to the directory and use this command: fasterq-dump SRR20073591.sra, I get an output file called SRR20073591.fastq….

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Differentially expressed circRNAs in peripheral blood samples as potential biomarkers and therapeutic targets for acute angle-closure glaucoma

Study approval and patient consent The study protocol was approved by the Ethics Committee of Qinghai Provincial People’s Hospital (approval number: 2023-141) and conducted in accordance with the ethical principles for medical research involving human subjects described in the Declaration of Helsinki in addition to relevant Chinese laws and institutional…

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Errors running genome polishing with Arrow

Errors running genome polishing with Arrow 0 Dear Biostars community, I am performing a genome polishing using Arrow, but I am getting errors immediately I launch the script. I have tried to use Arrow though gcpp version 2.0.2-2.0.2 (installed via bioconda), and using variantCaller version 2.3.3 Using gcpp, I got…

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rna-seq analysis with Salmon – how to Import and summarize using tximport

Hi! I’m trying to do RNA-seq analysis using salmon and would like to have a matrix of read counts of 10 RNA fastq files. I installed salmon with bioconda, however, I can only find version : 0.8.1 even after ‘conda update salmon’. So I have been doing with version 0.8.1…

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Perform Primer to Primer comparison to see and show if the primers produced are new or 100% similar to published primers

Blog:Perform Primer to Primer comparison to see and show if the primers produced are new or 100% similar to published primers 1 Hi Everyone I was recently asked to compare the primers we produced in our lab with the published primers and see if they are 100% similar or not….

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Installation – environment file not found – Technical Support

rjay428 (Rylee Jensen) September 5, 2023, 10:34pm 1 Hi all! Brand new to QIIME2 and with the Python environment as well. I’m running into an issue during the installation process that is close to what is posted on here, but I haven’t been able to figure out this exact problem….

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Building mosdepth on macOS

This is just a tiny tutorial on how to build mosdepth on Mac. There is currently no version for Mac available at conda (hope that changes soon, edit (3/2021): it did change, see anaconda.org/bioconda/mosdepth), and from what I’ve read building from source was a pain so far, still these simple…

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Failed installation of OpenMS

Failed installation of OpenMS 0 I have been trying to install OpenMS on my Ubuntu system. This is the command I’m using: conda install -c bioconda openms I keep getting this error: ————————————————————————————————————————————————————————————— Collecting package metadata (current_repodata.json): failed CondaHTTPError: HTTP 000 CONNECTION FAILED for url <conda.anaconda.org/conda-forge/noarch/current_repodata.json&gt; Elapsed: – An HTTP…

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Computer equipment for metagenomic analysis

Computer equipment for metagenomic analysis 2 Hello everyone, I am an undergraduate in a lab that does a lot of 16s amplicon sequencing. My lab does a lot of stuff with microbial source tracking and soil microbiome. For years, we have been doing analysis with the Ribosomal Database Project. RDP…

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Equipment for metagenomic analysis

Equipment for metagenomic analysis 0 Hello everyone, I am an undergraduate in a lab that does a lot of 16s amplicon sequencing. My lab does a lot of stuff with microbial source tracking and soil microbiome. For years, we have been doing analysis with the Ribosomal Database Project. RDP recently…

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a cross-platform, efficient, practical and pretty CSV/TSV toolkit

Tool:csvtk – a cross-platform, efficient, practical and pretty CSV/TSV toolkit 2 Hi all, I’d like to share my another practical toolkit, csvtk, after introducing SeqKit yesterday. Introduction Similar to FASTA/Q format in field of Bioinformatics, CSV/TSV formats are basic and ubiquitous file formats in both Bioinformatics and data sicence. People…

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Perbase base-depth

Perbase base-depth 2 Hi all, I hope everyone is doing great. may I ask if anyone knows how can I get perbase base-depth function? I have followed the instruction in github.com/sstadick/perbase and downloaded it by conda install -c bioconda perbase. The help function shows that only simple-depth function is included…

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Using Bioconda with Mac M1 Processor?

Hello Everyone! I’m extremely new to bioinformatics, so please understand my complete ignorance to this process. My lab use to utilize Michigan States Ribosomal Database Project (RDP), but it recently stopped being supported and is no longer available. We are attempting to pivot to QIIME 2 to clean up and…

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Insertion sequence transposition inactivates CRISPR-Cas immunity

Primers, plasmids, bacterial strains, and growth conditions Primers, plasmids, and strains used in this study are listed in Tables S1–S3, respectively. Escherichia coli strains MG1655, DH10B, MDS42, and their derivates were cultured in LB medium at 37 °C, with shaking at 220 rpm. All the recombinants containing the temperature-sensitive pSC101-derived plasmid were cultured…

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CamPype: an open-source workflow for automated bacterial whole-genome sequencing analysis focused on Campylobacter

Collins FS, Green ED, Guttmacher AE, Guyer MS. US National Human Genome Research Institute. A vision for the future of genomics research. Nature. 2003;422(6934):835–47. Article  CAS  PubMed  Google Scholar  Slatko BE, Gardner AF, Ausubel FM. Overview of next-generation sequencing technologies. Curr Protoc Mol Biol. 2018;122(1):e59. Article  PubMed  PubMed Central  Google…

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Issues with running featureCounts with STAR

Issues with running featureCounts with STAR 0 I am trying to generate a count table after aligning my CLIP-seq results to a genome index. I have been using several online tutorials, but I am running into an issue when using featureCounts from bioconda subread. I have tried referencing a folder…

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error installing SAMtools and bamtools

error installing SAMtools and bamtools 1 Hi everyone, I am trying to install samtools, Rsamtools and bamtools using Conda but I always get this error for both: Collecting package metadata (current_repodata.json): done Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): done Solving…

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Samtools Failing to Install through Conda

Samtools Failing to Install through Conda 2 Hi all, I just got a new laptop and am trying to work on some sequencing data and need to install samtools. On my old laptop, I was able to do this through conda using: conda install -c bioconda samtools However, when I…

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Why are the bioconda bioconductor packages so slow to update?

mamba 13 4,864 7.0 C++ The Fast Cross-Platform Package Manager Because conda is very slow at resolving dependencies. Mamba (github.com/mamba-org/mamba) is faster if that is your goal Sonar Write Clean C++ Code. Always.. Sonar helps you commit clean C++ code every time. With over 550 unique rules to find C++…

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Bioconda Utils – Open Source Agenda

bioconda-utils is a set of utilities for building and managing bioconda recipes. Since bioconda-utils is tightly coupled to bioconda-recipes, it is strongly recommended that bioconda-utils be set up and used according to the instructions at bioconda.github.io/contributor/index.html. This will ensure that your local setup matches that used to build recipes on…

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creating conda environment from snakemake rule

I am trying to activate a conda environment from snakemake to use a different environment for a rule in the workflow. I created a .yml file to specify dependencies. This is the snakemake rule I defined: rule Merge_VCFs: input: f1=’file1′ f2=’file2′ output: vcf=”output_file” conda: “bcftools_env.yml” shell: “”” bcftools merge -m…

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install failed: “location of failed script: /public/lihs/miniconda3/envs/qiime2-2023.5/bin/.bioconductor-genomeinfodbdata-post-link.sh” – Technical Support

Hi,I got a problem in qiime2 install using conda. It seems the R package bioconductor-genomeinfodbdata cannot be installed. Previously somebody posted similar issues, but were not well solved. I also tried to install bioconductor-genomeinfodbdata indenpendently but also failed, so I guess it should be some problem in this R package….

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macos – Cant install R-bioconductor-packages via anaconda

I wanted to start using conda evironments on my new computer, primarily for bioinformatic analysis. However, I can not bring it to download bioconductor packages. I tried several approaches right now, but could not accomplish a succesful installation. Installation I basically followed the instructions on this website Starting by downlaoding…

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failed with initial frozen solve. Retrying with flexible solve. PackagesNotFoundError: The following packages are not available from current channels:

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…

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hisat2-align exited with value 1

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…

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python – Snakemake wrappers suddenly stopped working

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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linkerror with installation – Technical Support

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…

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NanoSim Error “Please specify the training reads and its reference genome!”

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…

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Setting up conda channels – Sonatype Nexus Repository

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…

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QIIME2 2023.2 Installation error on *Linux* – Technical Support

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…

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r – First I had an error with GLIBCXX_3.4.30 and now I can’t create any more conda environments

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…

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conda install error with qiime2-2023.2 – Technical Support

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…

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How can I update fastq-dump to 3.0.0?

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…

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Rescript “ImportError” – Technical Support

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…

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MULTIQC problem

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…

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tophat2 installation error

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…

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The sleight-of-hand trick that can simplify scientific computing

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…

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ChIP-Seq experiment, MACS2 bdgpeakcall 0 fold-change, pvalue and qvalue

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…

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python – Samtools shared library libcrypto.so.1.0.0 not found

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 -…

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The power of accurate long-read RNA sequencing for fusion gene detection in cancer research

  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…

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error when attempting to install qiime2 2023.2 – Technical Support

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…

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Installation 2023.2 – Technical Support

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…

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Problem with fatsq-dump

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…

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Bioinformatics package

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…

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q2 galaxy: tiny upload job taking forever to run – Technical Support

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…

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Qiime2 2022.8 can’t be installed with mamba – Technical Support

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

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Nextflow Singularity/Apptainer error: command not found

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…

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Conda is installing older version of Spades even though latest version is there in the bioconda repository

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…

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sequence annotation – Barrnap Bacterial rRNA Predictor script permission denied error when running Prokka

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…

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conda create env using .yml file leads to dependency conflicts

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…

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Problems installing songbird with qiime2-2022.11 on Linux anaconda – User Support

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…

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samtools missin

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…

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The Biostar Herald for Wednesday, February 15, 2023

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…

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How to create Dockerfile without copying large data input and Build image such that snakemake wokflow run as Entrypoint

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…

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Containerization For Bioinformatics

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…

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Plugin error from aldex2, An error was encountered while running ALDEx2 in R (return code 1) – User Support

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…

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Error to install qiime2-2022.11 with conda on Mac – Technical Support

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…

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Mugsy not working

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…

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setting up Kallisto software

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…

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Analysis of Smart-Seq3 data with kallisto-bustools

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…

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cutadapt installed via conda igzip error for some fastq files

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 @…

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Using genelab-utils to download GeneLab workflows

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…

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ValueError: unsupported format character ‘T’ (0x54) at index 3312 when creating environment from environment file – Technical Support

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…

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Are package downgrades a necessary evil in Conda?

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…

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Building a Simulated Metagenomic Dataset

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…

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r – How can I install the Bioconductor package “liftOver” in a conda environment?

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…

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Installing ensembl-vep

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…

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Mapping reads using kallisto – rna seq analysis

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…

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Issue with streamlit as dependency when deploying my package to Bioconda repository – Using Streamlit

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…

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Unable to install bioconda packages in conda environments

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…

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installation of qiime2 on pycharm with anaconda interperter

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…

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Description, Programming Languages, Similar Projects of Bioconda Recipes

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…

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adRn-s/ukbbgwas – githubhot

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…

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Files :: Anaconda.org

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…

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python – samtools and trinity causing inconsistencies in conda env

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…

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python – Packages Not Found Error: Not available from current channel- Bioconda

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…

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conda samtools

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

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What do bioconda’s perl-net-ftp and perl-lwp-protocol-https do?

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: -…

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Bioconda faststructure – gitmetadata

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,…

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Mle Application With Gekko In Python

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…

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bioconda-recipes from iminkin – Github Help

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…

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python error :Conda channels

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…

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About QUAST

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…

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rust-bio-tools 0.35.0 – Docs.rs

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,…

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