Tag: conda

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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parallel-fastq-dump install failed

parallel-fastq-dump install failed 0 Good morning, I am trying to install parallel-fastq-dump but I failed. And here is what ssh sever say: conda install parallel-fastq-dump Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. PackagesNotFoundError: The following packages are not available from current…

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python – Scikit Learn _ufuncs error in Jupyter notebooks

Scikit learn has had _ufuncs errors for the past week and I can’t figure out why. I’m using python on anaconda and a Dell computer, while using Jupyter notebooks. It was previously fine until last week when I got these issues I’ve looked on other stack overflow questions and tried…

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Install Sklearn With Code Examples

Install Sklearn With Code Examples In this article, we will see how to solve Install Sklearn with examples. pip install scikit-learn The solution to the previously mentioned problem, Install Sklearn, can also be found in a different method, which will be discussed further down with some illustrative code. conda update…

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Jupyter Sagemath Kernel With Code Examples

Jupyter Sagemath Kernel With Code Examples In this session, we are going to try to solve the Jupyter Sagemath Kernel puzzle by using the computer language. The code that follows serves as an illustration of this point. mkdir -p /usr/local/share/jupyter/kernels ln -nsf /opt/SageMath/local/share/jupyter/kernels/sagemath /usr/local/share/jupyter/kernels/sagemath The Jupyter Sagemath Kernel was solved…

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How to install Biopython in Python

Table of Contents # Install Biopython on Windows Install Biopython on macOS or Linux Install Biopython in Visual Studio Code Install Biopython in PyCharm Install Biopython in Anaconda Install Biopython in Jupyter Notebook Install biopython on Windows # To install the biopython module on Windows: Type CMD in the search…

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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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How to use Scikit-Learn in Python [Complete Tutorial]

In this tutorial, we will focus on Scikit-Learn library usage in Python. Scikit-Learn is simple, fast and useful library used in python machine learning. It provides simple and efficient tools used in data analysis and data mining. Its free, easy to use and accessible to everyone. It is reusable in…

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Institut Pasteur de Dakar hiring Bioinformatics Analyst in Dakar, Senegal

We are looking for an enthusiastic and motivated bioinformatician to join the Epidemiology, Clinical Research, and Data Science department at the Institut Pasteur de Dakar. The selected candidate will develop and apply bioinformatics methods to support multiple projects in the area of next-generation sequencing and -omics. Minimum qualification Bachelor’s degree…

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Page Not Found – QIIME 2 Forum

Sign Up Log In Log In Popular installing qiime2 with conda – executing transaction timeoutUser Support Cannot run DADA2 in the tutorialsTechnical Support meta analysis and weird looking emperor plot of beta-analysisUser Support QIIME 2 2022.8 is now available!Announcements Qiime Plugin error from fragment-insertionTechnical Support [RESOLVED] Notice to Multi-User System…

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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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Introduction to HybridNets using PyTorch

In deep learning and computer vision, models tackle a specific task. For example, we can find models for image classification, object detection, and image segmentation also. But there are very few models out there which perform end-to-end vision perception on both, object detection and semantic segmentation. But one of the…

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Not enough memory on RTX 3090 to train ViTDet?

If you do not know the root cause of the problem, please post according to this template: Instructions To Reproduce the Issue: I’m trying to train an instance segmentation ViTDet model with a custom and relatively small dataset (6000 images of 640×480) I’m using Windows 10 and RTX 3090. I’m…

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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 – STAR error in snakemake pipeline: “EXITING because of FATAL ERROR: could not open genome file”

I’m trying to use a 2 pass STAR mapping strategy (also explained here informatics.fas.harvard.edu/rsem-example-on-odyssey.html), but I’m getting an error. I’ve read through this page [https://github.com/alexdobin/STAR/issues/181] and I have a similar issue, but the discussed solutions don’t seem to help. Perhaps this is more a snakemake issue rather than a STAR…

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ALDEx2 Plugin Error – Community Plugin Support

Ms-Tai (Taiquitha T. Robins) July 19, 2022, 2:49am #1 Plugin error from aldex2:An error was encountered while running ALDEx2 in R (return code 1), please inspect stdout and stderr to learn more.Debug info has been saved to /tmp/qiime2-q2cli-err-4j7_h2at.log lizgehret (Liz Gehret) July 19, 2022, 5:15pm #2 Hi @Ms-Tai, Please include…

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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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Scientist I, Bioinformatics job at Vir Biotechnology in United States – 53516780

Vir Biotechnology is a commercial-stage immunology company focused on combining immunologic insights with cutting-edge technologies to treat and prevent serious infectious diseases. Vir has assembled four technology platforms that are designed to stimulate and enhance the immune system by exploiting critical observations of natural immune processes. Its current development pipeline…

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Pytorch Foundation

pytorch yes Facebook Developed deep learning library . Details visible Official website . For the convenience of management , Usually in Anaconda or miniconda Create a new virtual environment installation in pytorch. New virtual environment (MacOS) Method 1 : direct Anaconda Navigator Install in stay Navigator>Environments Create a new environment…

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python – NotFittedError – Titanic Project Kaggle

I am trying different machine learning projects from Kaggle to make myself better. Here is the model that I am using: from sklearn.ensemble import RandomForestClassifier y = train_data[“Survived”] features = [“Pclass”, “Sex”, “SibSp”, “Parch”] X = pd.get_dummies(train_data[features]) X_test = pd.get_dummies(test_data[features]) model = RandomForestClassifier(n_estimators = 100, max_depth = 5, random_state =…

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Jupyter WebIO in binder – JupyterHub

I just learned how to run julia notebooks in binder. Now I want to use the PlotlyJS package in julia. Usually, when I need a package in julia on binder, I install it locally in a conda environment first and then copy Project.toml and Manifest.toml to my repository to start…

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How do I find all Sequence Lengths in a FASTA Dataset without using the Biopython

You really don’t need regular expressions for this. header = None length = 0 with open(‘file.fasta’) as fasta: for line in fasta: # Trim newline line = line.rstrip() if line.startswith(‘>’): # If we captured one before, print it now if header is not None: print(header, length) length = 0 header…

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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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Jupyter notebook not loading the correct virtual environment

We deployed Jupyterhub in Kubernetes using the helm chart , the chart version is 0.9.0 github.com/jupyterhub/zero-to-jupyterhub-k8s/tree/main/jupyterhub zero-to-jupyterhub.readthedocs.io/en/latest/jupyterhub/installation.html Users creating virtual environments using the terminal and created kernals as well, But when they accessing the jupyter notebook using the newly created kernal and run the command !conda info It is not…

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How do I install biopython in anaconda?

Package maintainers recommend using (in the terminal): conda install -c conda-forge biopython We deliberately recommend using Biopython from the conda-forge channel, as this is usually up to date and covers Windows, Mac OS X and Linux. The default Conda channel does have Biopython, but is often out of date. biopython.org/wiki/Packages…

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python – Install autodock vina via pip in Windows

I trying to install vina using pip and get this error: C:\Users\chase>pip install vina Collecting vina Using cached vina-1.2.3.tar.gz (95 kB) Installing build dependencies … done Getting requirements to build wheel … error ERROR: Command errored out with exit status 1: command: ‘D:\Anaconda\python.exe’ ‘D:\Anaconda\lib\site- packages\pip\_vendor\pep517\in_process\_in_process.py’ get_requires_for_build_wheel ‘C:\Users\chase\AppData\Local\Temp\tmpo4147jnr’ cwd: C:\Users\chase\AppData\Local\Temp\pip-install- x0_x1cyl\vina_418ca6103711445caf359fdf3574d54b…

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How to upgrade Kernel version? – JupyterHub

I have.a JupyterHub running in a local K8s cluster, deployed via KubeApps. It works like.a charm, except for the fact that it is running Python 3.7. I would like to upgrade it to Python 3.10. I tried to run conda update python and conda install -y python=3.10 from the notebook,…

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python – Pymc3 install issues on windows 10

So I downloaded pymc3 (uninstalled and reinstalled a few times) and every time I try to import pymc3 into a jupyter notebook I get some kind of error. I am guessing that I am having an issue with how I am installing Pymc3, I followed this tutorial: github.com/pymc-devs/pymc/wiki/Installation-Guide-(Windows). After my…

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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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which of the following are the prerequisite packages for scikit-learn?

Mohammed Guys, does anyone know the answer? get which of the following are the prerequisite packages for scikit-learn? from screen. Installing scikit There are different ways to install scikit-learn: Install the latest official release. This is the best approach for most users. It will provide a stable version and pre-built…

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Distributed training on slurm cluster – distributed

chinmay5 (Chinmay5) April 29, 2022, 12:48pm #1 Sorry for the naive question but I am confused about the integration of distributed training in a slurm cluster. Do we need to explicitly call the distributed.launch when invoking the python script or is this taken care of automatically? In other words, is…

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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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Postdoc / Research Scientist in Bioinformatics and Computational Genomics

Job Description Are you a computer geek with a strong interest in genomics? Do you want to use your computational skills to solve human diseases? At the Department of Neurology at Harvard Medical School and Brigham & Women’s Hospital, we have two vacant positions: postdoctoral fellow and research scientist in…

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Kaggle Machine Learning

In this article, we’ll learn step by step an entire process of machine learning to solve a challenge in Kaggle Competition and make a submission. We’ll explore through Kaggle Competition joining, Data Exploration, Feature Engineering, Model Training, Testing, Scoring, and Evaluation. Then, we’ll go ahead and submit our result to…

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Brew Conda Recipes

conda-forge community driven packaging for conda Recipes Details: About conda-forge. conda-forge is a GitHub organization containing repositories of conda recipes. Thanks to some awesome continuous integration providers (AppVeyor, Azure Pipelines, CircleCI and TravisCI), each repository, also known as a feedstock, automatically builds its own recipe in a clean and repeatable…

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Jupyterhub openshift with no S2I capability – Zero to JupyterHub on Kubernetes

Hi All I have searched lot in google but couldn’t find answer.we have openshift infrastructure available, but only limited functionalities.in that we’re not allowed to use S2I but only able to boost container via jenkins and run oc command there(jenkinsfile).problem we have now is we can’t even download jupyterhub image…

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Can’t locate Bio/SeqIO.pm – githubhot

Hi i am using MacOS Catalina, i am facing this error. i have tried through conda and CPAN to fix this. i am facing this error from last 2 weeks, Before this module was working . Can you guide me, How i can fix it. Can’t locate Bio/SeqIO.pm in @INC…

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Mapped reference id is not an id of the genome file genome_nowhitespace.fa

miRDeep2: Mapped reference id is not an id of the genome file genome_nowhitespace.fa 1 Hi everyone, I’m trying to run nf-co.re/smrnaseq pipeline and I’m having a problem with mirdeep2. Command: nextflow run nf-core/smrnaseq -profile ijcluster –input /home/794_both.fastq.gz –outdir /home/results –genome GRCh38 –protocol qiaseq –mature mirbase.org/ftp/CURRENT/mature.fa.gz –hairpin mirbase.org/ftp/CURRENT/hairpin.fa.gz Error message: Command…

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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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Running rstudio (but not R alone) inside of a conda environment complains about finding Rccp.so

I find that when I try to load some packages in a conda environement, when using rstudio (but not when I’m using R directly), I get an error message about a missing Rcpp.so file. I activate my conda environment (which is running R version 4.1), open RStudio (which I installed…

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[BioPython] ModuleNotFoundError: No module named Bio.PDB.SASA

[BioPython] ModuleNotFoundError: No module named Bio.PDB.SASA 2 Hello, I am trying to calculate the solvent accessible surface of pdb files using Biopython. Specifically I am trying to deduce the interaction surface of complex by substracting the solvent accessible surface of both unbound structure to the solvent accessible surface of the…

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CORS issues behind nginx ingress after updating to JupyterHub 2.1.1 – JupyterHub

Hi there, I noticed multiple issues after upgrading to JupyterHub 2.1.1 from 2.0.0. I stopped seeing spawn progress when starting the singleuser server. Logs: [I 2022-03-04 20:57:47.436 JupyterHub log:189] 302 GET /hub/spawn -> /hub/spawn-pending/konstantin.taletskiy@labshare.org (konstantin.taletskiy@labshare.org@192.168.15.108) 1006.02ms [I 2022-03-04 20:57:47.524 JupyterHub pages:405] konstantin.taletskiy@labshare.org is pending spawn [I 2022-03-04 20:57:47.528 JupyterHub log:189]…

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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 – PyTorch working in Miniconda but “not compiled with CUDA enabled” in PyCharm

I have had quite the journey trying to get PyCharm to use my GPU (NVIDIA GeForce GTX 1080 ti) when running code from this github: github.com/gordicaleksa/pytorch-neural-style-transfer After a whole lot of back and forth setting up CUDA, cuDNN etc., I have finally got PyTorch working (pretty sure) in my Miniconda…

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trollchu | coder – Coder Social

Qingzhao’s Projects AI-learns-to-play-the-dino-game AsFem A Simple Finite Element Method program (AsFem) aten Molecular / atomic coordinate editor atomman Atomistic Manipulation Toolkit awesome-python-chemistry A curated list of Python packages related to chemistry awesome-python-MD cantera Chemical kinetics, thermodynamics, and transport tool suite CFDPython A sequence of Jupyter notebooks featuring the “12 Steps…

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No such file or directory)

I have R(version 4.1.2) installed on Fedora35. When I tried to install “DESeq2”, I got the following warning. 1: .inet_warning(msg) : installation of package ‘genefilter’ had non-zero exit status 2: .inet_warning(msg) : installation of package ‘locfit’ had non-zero exit status 3: .inet_warning(msg) : installation of package ‘DESeq2’ had non-zero exit…

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nf-core/circrna

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data Introduction nf-core/circrna is a best-practice analysis pipeline for the quantification, miRNA target prediction and differential expression analysis of circular RNAs in paired-end RNA sequencing data. The pipeline is built using Nextflow, a workflow tool to run tasks across…

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Picrust2 not recognized – Community Plugin Support

Ok. So I’m doing this in a computing cluster for reference, and before doing anything I can see these conda environments: (base) [cjone228@jhu.edu@bc-login01 ~]$ conda env list # conda environments: # base * /home-1/cjone228@jhu.edu/miniconda3 picrust2 /home-1/cjone228@jhu.edu/miniconda3/envs/picrust2 qiime2-2019.10 /home-1/cjone228@jhu.edu/miniconda3/envs/qiime2-2019.10 qiime2-2019.7 /home-1/cjone228@jhu.edu/miniconda3/envs/qiime2-2019.7 qiime2-2020.2 /home-1/cjone228@jhu.edu/miniconda3/envs/qiime2-2020.2 qiime2-2020.6 /home-1/cjone228@jhu.edu/miniconda3/envs/qiime2-2020.6 Now when I try and install…

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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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java – GATK: HaplotypceCaller IntelPairHmm only detecting 1 thread

I can’t seem to get GATK to recognise the number of available threads. I am running GATK (4.2.4.1) in a conda environment which is part of a nextflow (v20.10.0) pipeline I’m writing. For whatever reason, I cannot get GATK to see there is more than one thread. I’ve tried different…

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Windows installing pytorch 0.3 – Stackify

The earliest available version on windows is 0.4.0 As can be seen when searching for the available version on conda. $conda search pytorch-cpu -c pytorch Loading channels: done # Name Version Build Channel pytorch-cpu 0.4.0 py35_cpuhe774522_1 pytorch pytorch-cpu 0.4.0 py36_cpuhe774522_1 pytorch pytorch-cpu 0.4.1 py35_cpuhe774522_1 pytorch pytorch-cpu 0.4.1 py36_cpuhe774522_1 pytorch pytorch-cpu…

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python – Trying to import scikit-learn to PyCharm on Mac M1

I wanted to install the sklearn package in PyCharm. However, I always got the same error (below is an extract): pip install scikit-learn # input Collecting scikit-learn Using cached scikit-learn-1.0.2.tar.gz (6.7 MB) Installing build dependencies … error error: subprocess-exited-with-error × pip subprocess to install build dependencies did not run successfully….

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Running Pymc3 fast posterior sample in a multi-node cluster getting stuck – Questions

I am running a pymc3 model multiple times in a loop to estimate posterior distributions, every iteration I change the data using pm.set_data with model: pm.set_data({“gw_pump_semi”: pump, “gw_pump_semi_lag”: pump_lag, “id_wtr_yr_lag”: [wtr_yr_lag]*2, “id_wtr_yr”: [wtr_yr]*2}) p_post = pm.fast_sample_posterior_predictive(trace=gwtrace,samples=400, random_seed=800,var_names=[“depth_like”])[“depth_like”] Before I start the parallel computing process I define the pm.model() as model…

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Pytorch cuda is unavailable even installed CUDA and pytorch with cuda. How to fix?

My environment is (Ubuntu 20.04 with NVIDIA GTX 1080Ti): $ nvidia-smi | grep CUDA | NVIDIA-SMI 470.74 Driver Version: 470.74 CUDA Version: 11.4 | $ nvcc -V nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2021 NVIDIA Corporation Built on Sun_Aug_15_21:14:11_PDT_2021 Cuda compilation tools, release 11.4, V11.4.120 Build cuda_11.4.r11.4/compiler.30300941_0 After…

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python – Error when trying to install autodocking Vina

I’m trying to install Autodock Vina with pip command. But when I run the command pip install -U numpy vina: I get a the following error: Collecting vina Using cached vina-1.2.3.tar.gz (95 kB) Installing build dependencies … done Getting requirements to build wheel … error error: subprocess-exited-with-error × Getting requirements…

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How to run pytorch with NVIDIA “cuda toolkit” version instead of the official conda “cudatoolkit” version?

You can try to install PyTorch via Pip: pip install torch torchvision It is also official way of installing, available in “command helper” at pytorch.org/get-started/locally/. It uses preinstalled CUDA and doesn’t download own CUDA Toolkit. Also you can choose the version of CUDA to install PyTorch for: pip install torch==1.7.1+cu110…

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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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have trouble in installing biopython package

I would suggest the root of your problem is this line: /usr/libexec/gcc/powerpc-apple-darwin10/4.2.1/as: assembler (/usr/bin/../libexec/gcc/darwin/ppc/as or /usr/bin/../local/libexec/gcc/darwin/ppc/as) for architecture ppc not installed XCode 4 doesn’t like trying to compile things with the PPC architecture, so you need to stop it trying: env ARCHFLAGS=”-arch i386 -arch x86_64″ python setup.py install (DISCLAIMER: I…

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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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[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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Why can’t I change my python version

Why can’t I change my python version 0 I am using some bioinformatics software that requires a python2 environment. I use conda to create a new environment and specify the python version as 2.7.18, but when I type ‘python’ I find that the python version is 3.9.5. I use the…

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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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