Tag: conda

[pytorch/torchx] slurm: environment improvements

The current slurm scheduler specifies the working directory via the image field of the Role. This doesn’t match how any of the other schedulers work since local_cwd has been switched to use the current working directory. We should update the slurm scheduler to be more inline with the other schedulers….

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variant – Where should you put you cache for ensembl-vep using conda

I’ve installed vep in conda like so: conda install ensembl-vep=105.0-0 And then I installed the human cache like so: vep_install -a cf -s homo_sapiens -y GRCh38 -c /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/refs/vep –CONVERT But when I try and run vep I get an error: vep –dir_cache /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/refs/vep -i /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/data/test/manual/results/variants/cohort.norm_recalibrated.vcf -o /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/data/test/manual/results/variants/cohort.norm_recalibrated_vep.vcf Am I doing…

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H2O is an in-memory platform for distributed, scalable machine learning

H2O is an in-memory platform for distributed, scalable machine learning. H2O uses familiar interfaces like R, Python, Scala, Java, JSON and the Flow notebook/web interface, and works seamlessly with big data technologies like Hadoop and Spark. H2O provides implementations of many popular algorithms such as Generalized Linear Models (GLM), Gradient…

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Fail to install Ensembl VEP

Fail to install Ensembl VEP 2 Hello I have been encounter some issues on installing the Ensembl VEP. I am using Ubuntu 20.04 system, with the newest perl v5.34. perl -MBio::Root::Version -e ‘print $Bio::Root::Version::VERSION,”n”‘ 1.006924 However, when I install the VEP, it failed. Hello! This installer is configured to install…

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traviz 1.0.0 installation fails: ERROR: lazy loading failed

Hi, I cannot install traviz package (version 1.0.0) from Bioconductor on a linux machine (from source). I have a conda environment, and I installed traviz from conda, but it cannot be used – when I do library(traviz) R just crashes and quits without any message. So I tried to install…

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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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error while loading shared libraries

Question: Question: bowtie2-align-s: error while loading shared libraries Abhinav26 days ago Question: bowtie2-align-s: error while loading shared libraries /home/emilyw/.conda/envs/shotgun_134/bin/bowtie2-align-s: error while loading shared libraries: libtbb.so.2: cannot open shared object file: No such file or directory (ERR): Description of arguments failed! Exiting…

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Installation issues with PyMC3 – Stackify

Just had this problem and found a solution. When searching (with Bing or Google) for conda install of pymc3, several links come up. The first is with conda-forge: conda install -c conda-forge pymc3 DO NOT USE THIS or you will get the error messages in the above posts. I have…

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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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python – Missing input files after defining them in function

I am trying to do QC on RNAseq data that is tarballed. I am using Snakemake as a workflow manager and am aware that Snakemake does not like one-to-many rules. I defining a checkpoint would fix the problem but when I run the script I get this this error message…

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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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‘dataspell’ tag wiki – Stack Overflow

JetBrains DataSpell is an IDE for data science with intelligent Jupyter notebooks, interactive Python scripts, and lots of other built-in tools. The IDE for Professional Data Scientists DataSpell is an Integrated Development Environment (IDE) that is dedicated to specific tasks for exploratory data analysis and prototyping ML (machine learning)…

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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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error related to module

error related to module 0 I am trying to run a code but its showing this error. the error: INFO – Loading model INFO – Preparing genotype dosages INFO – Setting whitelist from available models INFO – Processing genotypes INFO – Preparing prediction INFO – Could not import HDF5 expression…

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Linux for Biologists e-book is free for one more week

News:Linux for Biologists e-book is free for one more week 1 Hi all, I wrote this book for students and researchers in biological sciences who are new to Linux. I believe some topics discussed might be useful for beginners in Bioinformatics as well. Free download (on Leanpub, ends June 6)…

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Biopython Contact Us | Contact Information Finder

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…

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r-bioc-basilisk — Freezing Python Dependencies Inside Bioconductor Packages

On Sun, Sep 19, 2021 at 03:45:57PM -0500, Dirk Eddelbuettel wrote: > > | I’m thinking about a “fake-basilisk” like r-cran-bh or r-bioc-zlib. > > I had a similar thought. I am also friends with the author of it. > > They are doing ‘The Right Thing’ there for _their_…

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Bug#991859: BioConductor MOFA2 needs basilisk

Hi Dirk, On Sun, Sep 19, 2021 at 03:45:57PM -0500, Dirk Eddelbuettel wrote: > > | I’m thinking about a “fake-basilisk” like r-cran-bh or r-bioc-zlib. > > I had a similar thought. I am also friends with the author of it. > > They are doing ‘The Right Thing’ there…

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Gromacs Contact Map | Contact Information Finder

Listing Results Gromacs Contact Map Contact maps using Gromacs ResearchGate Just Now Researchgate.net View All Contact maps using Gromacs ? I used gmx mdmat in gromacs to create contact maps, but it seems that the mdmat gives the minimum average distance rather than the average centre-of-mass distance. Estimated Reading Time:…

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Biopython Contact Map | Contact Information Finder

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….

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pandas – DataFrame to CSV save error on Kaggle Python. How to solve?

I’m trying to save a dataframe containing 20 million rows to a CSV format, with this: df_merge.to_csv(‘processed.csv’) After executing the code, I got this error message: OSError: [Errno 30] Read-only file system: ‘processed.csv’ What is this and how can I handle it? NOTE: The code is run on kaggle. Complete…

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deepmind alphafold github

The program handily beat all competitors, in what one . This will allow us to run alphafold only using CPU ( which is what our VM has). From the developers’ original publication: “The provided inference . The AlphaFold method. Found insideThis book constitutes the refereed proceedings of the First International…

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Install alphafold on the local machine, get out of docker.

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…

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alphafold colab github

for the third time worked! Found inside – Page iiThe eight-volume set comprising LNCS volumes 9905-9912 constitutes the refereed proceedings of the 14th European Conference on Computer Vision, ECCV 2016, held in Amsterdam, The Netherlands, in October 2016. Please make sure you have a large enough hard drive space, bandwidth…

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Bioinformatics Scientist Job Opening in Iowa City, IA at Jones Microbiology Institute Inc

Description: JMI Laboratories is a mid-sized company based in North Liberty, IA. A global leader for twenty years in anti-infectives research, JMI monitors annual changes in antibiotic resistance patterns through the SENTRY Antimicrobial Surveillance Program, serves as a clinical and reference laboratory in support of new drug development, and conducts…

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Align fastq SOLiD data

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,…

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Can’t locate Bio/SeqIO.pm – path error?

Can’t locate Bio/SeqIO.pm – path error? 0 Hi, I am trying to run snippy on my UBUNTU18 (inside a conda env that has this tool installed) but am getting an error: Can’t locate Bio/SeqIO.pm in @INC (you may need to install the Bio::SeqIO.pm module) I checked the posts here, and…

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Finding the significance of the overlap between 2 or more gene sets using simulation in R.

TLDR: Example R function to calculate significance of overlap of 2 or more gene sets. genes_all is a vector that contains all genes, and gene_sets takes a list of vectors for each gene set. I encourage people to read the full tutorial and attempt to reproduce the code themselves (especially…

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How to build and run a docker container with multiple conda envs – General Discussions

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…

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Downloading Files In Kaggle Gives

What if the grid variables in the source dataset DON’T share the same axis variables? Projected Gridded Data; Data Types; Media Files; AWS S3 Files; NcML; NCO. We use cookies on Kaggle to deliver our services analyze web traffic and improve your experience on the site. By using Kaggle you…

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Error: NCBI C++ Exception – Invalid choice selection: NCBI-Seqalign::Score.value.real

Error: NCBI C++ Exception – Invalid choice selection: NCBI-Seqalign::Score.value.real 1 Hi, I am having issues running blast from command line, accessing remote databases. This is what i am running: blastn -db nt -query {input} -out {output} -evalue 0.001 -max_target_seqs 100 -remote Which returns this: Error: NCBI C++ Exception: T0 “/opt/conda/conda-bld/blast_1559335677723/work/c++/src/objects/seq/../seqalign/Score_.cpp”,…

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How to install hisat2 on Mac OS Big Sur

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…

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PROVEAN not working

PROVEAN not working 2 Hello All, I’m having troubles making PROVEAN work. I’m getting this error while trying to run PROVEAN /gpfs01/home/x/NCBI-BLAST/blastdb/ftp.ncbi.nih.gov/blast/db/nr [17:44:08] searching related sequences… [18:45:32] clustering subject sequences… ./provean.sh: line 187: 41879 Segmentation fault $COMMAND Any idea what I’m doing wrong? provean • 652 views • link updated…

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Setup my Github repo in a Kaggle environment – Freelance Job in Machine Learning – $50 Fixed Price, posted September 1, 2021

I would like step by step instructions to: 1. Set up Git so that commands like “git pull” work within the provided linux environment 2. Create a Conda environment (or overwrite the existing one) in this Kaggle environment, generated from my own environment.yml file 3. Preserve all of this so…

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Setup my Github repo in a Kaggle environment | Python

I would like step by step instructions to: 1. Set up Git so that commands like “git pull” work within the provided linux environment 2. Create a Conda environment (or overwrite the existing one) in this Kaggle environment, generated from my own [login to view URL] file 3. Preserve all…

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Building Docker images

If you wonder what an image and a container is, please see : Building an image starts from a Dockerfile which is a plain text file with instructions. Here an example which we are going to build: It is based on the mambaforge image, so mamba is already installed which…

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Request for the process about install ‘fastANI’ on MacOS

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…

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installing samtools with conda – overcoming two common errors

Tutorial:installing samtools with conda – overcoming two common errors 3 Posting this here to help others. Question – trying to install samtools with conda and encountering this error: samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory or this error: samtools: error…

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Snakemake-Aligment using BWA-MEM2

Hello I have started using snakemake 6.5.2 to align fastq files with reference file. I have pasted the error below in this question. How to allocate memory in the snakefile and read the header from samfile, ‘-‘. This is the snakefile (wrapper for running alignment): rule bwa_mem2_mem: input: reads=[“/scicore/home/cichon/GROUP/test_workflow/samples/{sample}.1.fq”, “/scicore/home/cichon/GROUP/test_workflow/samples/{sample}.2.fq”]…

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Conda has been installed – but can’t be found file

Conda has been installed – but can’t be found file 1 You downloaded the installer, but did not install conda itself. Type: ./Miniconda3-latest-Linux-x86_64.sh …and follow the instructions on screen. Login before adding your answer. Traffic: 1082 users visited in the last hour Read more here: Source link

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Pybedtools error sans

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,…

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how to install conda bcftools +fill-tags plugin ?

how to install conda bcftools +fill-tags plugin ? 0 Hi, I am very new to bioinformatics but I wanted to know is there a way to install bcftools +fill-tags plugin in conda env. Plz consider that when I check my env there is not a bcftools folder and subsequently the…

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Create de novo repeat library

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…

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Issue reading fasta file with Biopython

Hello everyone, This should be very easy and I know it, but I am stuck with it and I cannot pinpoint my mistake. I wanted a boolean python function to check if a given file is in fasta format. And this, without manually checking myself the extension (.fa, .fasta etc)….

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VcfSampleCompare – empty output with warnings

Hello to all, I have 10 vcf files – 5 female fish and 5 male fish, I have merged all 10 fish to one vcf file.(all_fish.vcf) I performed the VcfSampleCompare analysis on ‘all_fish.vcf’ , following this:github.com/hepcat72/vcfSampleCompare The example command : vcfSampleCompare.pl –sample-group ‘wt1 wt2 wt3’ –sample-group ‘mut1 mut2 mut3’ input.vcf…

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terminal can’t activate base automatically (conda)

terminal can’t activate base automatically (conda) 0 hello everyone, the base suddenly can‘t be activated automatically when I start terminal, it can work before. I have to type bash to activate base now. I have tried conda config –set changeps1 true conda config –set auto_activate_base true but they didn’t work…

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Bioinformatics Software Engineer, Cancer Genomics Research Laboratory (req2036) job with Frederick National Laboratory

PROGRAM DESCRIPTION We are seeking an enthusiastic, creative, and collaborative bioinformatics software engineer to support pipeline development and analysis for our broad portfolio of genomic studies. If you have experience designing and deploying robust, reproducible, production-quality pipelines, then come join our talented team of bioinformaticians dedicated to understanding the genetics…

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zsh: exec format error: bigWigToWig

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…

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Error when trying to run IGV on server

Error when trying to run IGV on server 1 I want to use IGV on a server so I don’t have to download bam files to my local machine. I used conda to install igvtools. When I type igvtools in the command line I get this error: Using system JDK….

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