Tag: Anaconda

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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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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New Best Practices — Visual Studio Magazine

The Data Science Lab Binary Classification Using PyTorch, Part 1: New Best Practices Because machine learning with deep neural techniques has advanced quickly, our resident data scientist updates binary classification techniques and best practices based on experience over the past two years. By James McCaffrey 10/05/2022 A binary…

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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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How to activate a specific Python environment as part of my submission to Slurm?

You mean to activate a specific Python environment as part of your submission to Slurm? This is what I add to my job script and it works well. Note that I use Anaconda, which by default adds the required paths to my .bashrc script after installation. Hope this helps. …….

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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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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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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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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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Tutorial: How to Connect Jupyter Notebooks to Ocean for Apache Spark – The Spot by NetApp Blog

Jupyter Notebook is a web-based interactive computational environment for creating notebook documents. It supports programming languages – such as Python, Scala, R – and is largely used for data engineering, data analysis, machine learning, and further interactive, exploratory computing. Think of notebooks like a developer console or terminal, but with…

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Pymc3 linker error – v3

Hi all,I have been using pymc3 for about a year. A few months ago I changed from an intel mac to an M1 mac. Suddenly, I can’t use pymc3 anymore. I keep getting the following error that I have no idea how to interpret: You can find the C code…

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Install Jupyter Notebook on Debian 11 Bullseye Linux

Tutorial to learn the steps involve in the installation of Jupyter Notebook on Debian 11 Bullseye using command terminal. What is Jupyter Notebook? The Jupyter Project is a non-profit initiative that aims to develop and provide open-source software and open standards for interactive work. One of the most famous products…

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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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transcriptome – How to combine multiple .fasta files of primary assembly from Ensembl into one for sequence alignment?

I have some marmoset snRNA reads that I want to align with the reference transcriptome using cellranger. The primary assembly for marmoset is available here, which is broken down into 22 parts. However, cellranger mkref only accepts one .fa file to generate the transcriptome. I tried concatentaing all the extracted…

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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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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 – Biopython cannot export numpy

I am trying to use Biopython using anaconda and the Jupiter notebook with Python3. However, simply import numpy gives the following error: ————————————————————————— ImportError Traceback (most recent call last) File /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/core/__init__.py:23, in <module> 22 try: —> 23 from . import multiarray 24 except ImportError as exc: File /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/core/multiarray.py:10, in <module>…

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Importing matplotlib.pyplot in Rstudio using reticulate

I had similar issues. I did following and it solved. Before that I would like to refer you in following threads from where I got the solution… Qt platform plugin issue Rstudio PyQt5 – Failed to load platform plugin “windows”. Available platforms are: windows, minimal Here is what you have…

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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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import – How to make a python module accessible to multiple editors?

I am learning biopython and would like to use Visual Studio Code (VSC—my favorite editor so far) to do coding exercises on the topic. However, the module does not show up when I try to import using VSC. In fact, for my computer the biopython module only works in Spyder….

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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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linux – How to fix Perl from anaconda not installing bioperl? Bailing out the installation for BioPerl

vep -i examples/homo_sapiens_GRCh38.vcf –database Can’t locate Bio/PrimarySeqI.pm in @INC (you may need to install the Bio::PrimarySeqI module) (@INC contains: /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0/modules /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0 /home/youssef/anaconda3/envs/ngs1/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/youssef/anaconda3/envs/ngs1/lib/site_perl/5.26.2 /home/youssef/anaconda3/envs/ngs1/lib/5.26.2/x86_64-linux-thread-multi /home/youssef/anaconda3/envs/ngs1/lib/5.26.2 .) at /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Slice.pm line 75. BEGIN failed–compilation aborted at /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Slice.pm line 75. Compilation failed in require at /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Feature.pm line 84. BEGIN failed–compilation aborted at /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Feature.pm…

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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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GEMINI ISSUE

Using gemini found at: /usr/local/bin/gemini /usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/config.py:61: YAMLLoadWarning: calling yaml.load() without Loader=… is deprecated, as the default Loader is unsafe. Please read msg.pyyaml.org/load for full details. config = yaml.load(in_handle) CADD scores are being loaded (to skip use:–skip-cadd). GERP per bp is being loaded (to skip use:–skip-gerp-bp). Traceback (most recent call last):…

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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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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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cellranger count DETECT_COUNT_CHEMISTRY (failed)

cellranger count DETECT_COUNT_CHEMISTRY (failed) 0 I am learning scRNA-seq and the tutorial I follow uses dataset (1k pbmcs from healthy donor) from 10X genomics website. I downloaded fastq and reference transcriptome files and ran following command. cellranger-6.1.1/cellranger count –id pbmc_1k_v2_example –transcriptome /home/murat/Share/single_cell/refdata-gex-GRCh38-2020-A –fastqs /home/murat/Share/single_cell/pbmc_1k_v2_fastqs I get following message. Martian Runtime…

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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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Cellranger untar error

Cellranger untar error 1 [SOLVED] Hello I am trying to install Cellranger. I downloaded the tar file from 10X genomics website and wanted to untar that. However I am getting bunch of these errors. It fails to untar. Below is the line I use for unpacking. I am on windows…

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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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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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Get chromosome sizes from fasta file

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

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