Tag: SQLite

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 Mensur Dlakic, Istvan Albert, and was edited…

Use of data packages in containers 0 @893555ac Last seen 7 hours ago Germany For the Galaxy project we build quite a few containers that contain data packages (I hope I use the correct terms here) like bioconductor-org.Hs.eg.db. Often it’s many of such data packages which leads to large container…

I am currently building JupyterHub on single machine using Docker, and I want users to access a page where they can select the Docker image they want upon logging in, like the below page. But whenever I log in using any account, the system always redirects me to the JupyterLab…

I want to create a database for efficient queries, but using with targets. Is there a better alternative to open and close connection? tar_target(database, format = “file”, command = { db_file_name <- Sys.getenv(“DB_PATH”, “database.sqlite”) db <- dbConnect(SQLite(), db_file_name) dta_to_db(db, crsp_daily, “crsp_daily”) dta_to_db(db, crsp_monthly, “crsp_monthly”) dta_to_db(db, analist_coverage, “analist_coverage”) dbwriteTable(db, industry_classification, “industry_classification”)…

The hub on the host severed directly on my machine (not via docker image). I run the jupyterhub with command arg –debug, and got the terminal infomation as follows: root@DESKTOP-L60P4Q8:~/my_docker/main# jupyterhub –debug -f ../jupyterhub_config.py [D 2023-12-07 23:00:23.417 JupyterHub application:908] Looking for ../jupyterhub_config in /root/my_docker/main [D 2023-12-07 23:00:23.417 JupyterHub application:929] Loaded…

Hello, I’ve recently started a position responsible for a JupyterHub installation as part of an HPC environment; the old team left without leaving much in the way of documentation, and I’ve never worked on JupyterHub before, so please bear with me. When launching JupyterHub, the system will stay on the…

We are looking for a machine learning researcher with expertise in training the Llama 2 Large Language Model (LLM) using custom Hugging Face datasets. The specialist should have a deep understanding and experience in using PyTorch to speed up inference on Llama 2. Focus of the project: – The project…

Want to improve this question? Add details and clarify the problem by editing this post. I have a project that uses conda env with old pytorch version. It works smoothly if I use Nvidia V100, but it won’t run on other GPUs (I’ve tried RTX3080, TeslaA10, RTX2080TI, TeslaA2, TeslaT4) using…

Image by Gerd Altmann from Pixabay For downloading data and standardized metadata from GEO (Gene Expression Omnibus) and SRA (Sequence Read Archive), several bioinformatics and command-line tools and scripts are available, primarily hosted on GitHub. ARA: An automated pipeline developed for better sampling of NCBI SRA database records, allowing full…

Hello, members. Could someone tell me about hub.db.type database feature? Zero to JupyterHub with Kubernetes Configuration Reference The JupyterHub Helm chart is configurable by values in your config.yaml. In this way, you can extend user resources, build off of different Docker images, manage security and authentication, and mo… What pod…

AbbVie’s Genomics Research Center Computational Genomics is looking for a highly motivated computational biologist (Senior Scientist II, Bioinformatics) to join a team of bioinformatics scientists investigating aging and age-related diseases. AbbVie’s GRC is a center of excellence for bioinformatics, functional genomics, and human genetics. The GRC works across all R&D…

Hello, I’m trying to compile pytorch from source and encountering the following build error. $ CC=gcc-10 CXX=g++-10 python setup.py develop … [5995/6841] Linking CXX executable bin/HashStoreTest Warning: Unused direct dependencies: /home/netfpga/research/collective/pytorch/build/lib/libc10.so /home/netfpga/anaconda3/envs/pytorch_base/lib/libmkl_intel_lp64.so.1 /home/netfpga/anaconda3/envs/pytorch_base/lib/libmkl_gnu_thread.so.1 /home/netfpga/anaconda3/envs/pytorch_base/lib/libmkl_core.so.1 /lib/x86_64-linux-gnu/libdl.so.2 /home/netfpga/anaconda3/envs/pytorch_base/lib/libgomp.so.1 [5996/6841] Performing build step for ‘nccl_external’ FAILED: nccl_external-prefix/src/nccl_external-stamp/nccl_external-build nccl/lib/libnccl_static.a /home/netfpga/research/collective/pytorch/build/nccl_external-prefix/src/nccl_external-stamp/nccl_external-build /home/netfpga/research/collective/pytorch/build/nccl/lib/libnccl_static.a cd /home/netfpga/research/collective/pytorch/third_party/nccl/nccl &&…

Introduction When it comes to machine learning, having relevant and high-quality datasets is crucial for training and testing algorithms. However, finding suitable datasets can sometimes be a daunting task. Fortunately, there are several resources available that offer a wide range of public datasets for machine learning purposes. In this article,…

I am working on kaggle notebook to clean a dataset using SQL. I intent to convert the ‘Saledate’ column of table ‘housing’ which has timestamp to date datatype. below is the code # This Python 3 environment comes with many helpful analytics libraries installed # It is defined by the…

Data Reading read_csv(“/filename”, skip = value)Reads default csv’s and skips the value number of rows. Library(readr) read_tsv(“/filename”, skip = value)Reads default tab seperated sheets and skips value number of rows. Library(readr) read_delim(“/filename”,delim = “delimiter”, col_names = FALSE)General reading function, specifying the delimiter, saying we have no column names to assign…

I implemented JupyterHub using a Helm chart on a local Kubernetes cluster on VMware virtual machines. I want to cull users after they have been inactive for a while, but it seems not to work. This error log from the hub pod (pod named hub-545895f988-vmj2k) might be related: [W 2023-11-09…

Hi ! I try to mount a jupyterhub container. The server seems to run smoothly but cannot create a user notebook container (DockerSpawner). After a few seconds, the container disappears. Hereafter is my jupyterhub log (user: donzel): [D 2023-11-03 14:18:16.039 JupyterHub application:908] Looking for /srv/jupyterhub/jupyterhub_config in /srv/jupyterhub [D 2023-11-03 14:18:16.054…

Good afternoon, I am trying to do a DTU analysis for my research, but I am kinda new to this stuff and I have some problems. In particular on point 5). I am following the workflow of Bioconductor vignette rnaseqDTU and my pipeline is this: 1) read salmon quants ##…

In this tutorial we learn how to install r-cran-rsqlite on Ubuntu 22.04. r-cran-rsqlite is Database Interface R driver for SQLite Introduction In this tutorial we learn how to install r-cran-rsqlite on Ubuntu 22.04. What is r-cran-rsqlite r-cran-rsqlite is: This package embeds the SQLite database engine in R and provides an…

Zero to JupyterHub with Kubernetes uses by default SQLite as the database (source: Configuration Reference — Zero to JupyterHub with Kubernetes documentation). This default database is stored in a default Persistent Volume Claim defined in github.com/jupyterhub/zero-to-jupyterhub-k8s/blob/4103cfe1089a3f6df69b0fae97442be183ae5e12/jupyterhub/templates/hub/pvc.yaml. The documentation says By default, this disk is created by the cloud provider using…

Overview Associate Bioinformatics Data Manager US Remote The Emmes Company, LLC (“Emmes”) is a global, full-service Clinical Research Organization dedicated to excellence in supporting the advancement of public health and biopharmaceutical innovation. We believe in the power of truth, so much so that we named our company Emmes, which means…

R: SQLite transaction management sqlite-transaction {RSQLite} R Documentation SQLite transaction management Description By default, SQLite is in auto-commit mode. dbBegin() starts a SQLite transaction and turns auto-commit off. dbCommit() and dbRollback() commit and rollback the transaction, respectively and turn auto-commit on. DBI::dbWithTransaction() is a convenient wrapper that makes sure that…

AbbVie’s Genomics Research Center Computational Genomics is looking for a highly motivated computational biologist (Senior Scientist II, Bioinformatics) to join a team of bioinformatics scientists investigating aging and age-related diseases. AbbVie’s GRC is a center of excellence for bioinformatics, functional genomics, and human genetics. The GRC works across all R&D…

AbbVie’s Genomics Research Center Computational Genomics is looking for a highly motivated computational biologist (Senior Scientist II, Bioinformatics) to join a team of bioinformatics scientists investigating aging and age-related diseases. AbbVie’s GRC is a center of excellence for bioinformatics, functional genomics, and human genetics. The GRC works across all R&D…

Context k8s: v1.27.6helm: v3.13.0jupyterhub helm chart: 3.1.0 # configs.yaml proxy: service: type: NodePort ingress: enabled: true annotations: kubernetes.io/ingress.class: nginx nginx.ingress.kubernetes.io/proxy-body-size: 512m cert-manager.io/cluster-issuer: letsencrypt-prod hosts: – xxxxxxxxxxxxxxxxxxxxxxxx tls: – hosts: – xxxxxxxxxxxxxxxxxxxxxxxx secretName: codebook-tls singleuser: startTimeout: 300 debug: enabled: true Deployment seems to work fine: NAME READY STATUS RESTARTS AGE continuous-image-puller-2v74w…

In today’s data-driven world, the interface between SQL (Structured Query Language) and R has become a must-have for data professionals. SQL empowers us to efficiently interact with relational databases, while R programming language is versatile for data analysis. Combining these two powerful tools can dramatically increase your data conversion capabilities….

R dbWriteTable — RSQLite Functions for writing data frames or delimiter-separated files to database tables. RSQLite::dbWriteTable is located in package RSQLite. Please install and load package RSQLite before use. ## S4 method for signature ‘SQLiteConnection,character,data.frame’ dbWriteTable( conn, name, value, …, row.names = pkgconfig::get_config(“RSQLite::row.names.table”, FALSE), overwrite = FALSE, append = FALSE,…

I have installed z2jh on a local k8s cluster. Sometimes I get 500 error, other times it works fine.I’m using jupyterhub Version 3.0.0, helm chart 2.0.0 500 : Internal Server ErrorThe error was:Failed to connect to Hub API at ‘hub:8081/hub/api’. Is the Hub accessible at this URL (from host: jupyter-hammad-20ali-20baig)?…

Back in the days @minrk was contributing/maintaining the jupyter-deploy-docker repo, the docker-compose setup used a Postgres DB container: Then @manics simplify that, and the DB in compose was gone: I cloned and started using @minrk version, with the DB-container, at somepoint in 2021. It is still doing its humble and…

Description Diese Bibliothek enthält die Java-Server-Definition der OpenApi-Schnittstelle für die Schulverwaltungssoftware in NRW <dependency> <groupId>de.svws-nrw</groupId> <artifactId>svws-openapi</artifactId> <version>0.7.5</version> </dependency> <?xml version=”1.0″ encoding=”UTF-8″?> <project xsi:schemaLocation=”http://maven.apache.org/POM/4.0.0 maven.apache.org/xsd/maven-4.0.0.xsd” xmlns=”http://maven.apache.org/POM/4.0.0″ xmlns:xsi=”http://www.w3.org/2001/XMLSchema-instance”> <!– This module was also published with a richer model, Gradle metadata, –> <!– which should be used instead. Do not delete the following…

Why dbConnect GEOmetadb_demo.sqlite shows some information while dbConnect GEOmetadb.sqlite shows no information 0 sqlfile_demo <- getSQLiteFile(destdir = “~/bin/Rpack”, destfile = “GEOmetadb.sqlite_demo.gz”,type=”demo”) con <- dbConnect(SQLite(),sqlfile_demo) getBiocPlatformMap(con)[1:5,] output: title gpl bioc_package manufacturer 1 [Maize] Affymetrix Maize Genome Array GPL4032 Affymetrix 2 Agilent-026652 Whole Human Genome Microarray 4x44K v2 (Probe Name version) GPL13497…

Structural clustering algorithm The clustering procedure is similar to MMseqs2’s clustering but, instead of using sequences, Foldseek’s 3Di alphabet (Extended Data Fig. 1) was used to represent the structures as one-dimensional sequences. The clustering algorithm combines Linclust17 and cascaded MMseqs2 (ref. 42) clustering. The pipeline applies this strategy to allow for efficient…

Source: Rstudio.com Are you a data analyst or a data scientist looking to import a dataset into R for analysis? Look no further! In this article, we will guide you through the process of importing a data set into R, step by step. R is a powerful programming language and…

I attempt to force scopes with z2jh hub config here hub: loadRoles: jupyterdevs: groups: [JupyterDevs] scopes: [admin-ui, admin:users, admin:servers, tokens, admin:groups, list:services, read:services, read:hub, proxy, shutdown, access:services, access:servers, read:roles, read:metrics] … I provide groups from my authenticator, my extra spawner config is below. I also force the auth_model into admin…

    When it comes to managing and manipulating data in relational databases, Structured Query Language (SQL) is the biggest name in the game. SQL is a major domain-specific language which serves as the cornerstone for database management, and which provides a standardized way to interact with databases. With data…

DOI: 10.18129/B9.bioc.biodb   biodb, a library and a development framework for connecting to chemical and biological databases Bioconductor version: Release (3.17) The biodb package provides access to standard remote chemical and biological databases (ChEBI, KEGG, HMDB, …), as well as to in-house local database files (CSV, SQLite), with easy retrieval…

RStudio, a premier integrated development environment (IDE) for R programming language, has established itself as an indispensable tool for statisticians, data scientists and researchers. With its user-friendly interface, it provides powerful coding tools and makes the process of data analysis and visualization simpler and more effective. Its wide range of…

Source: nutsqlite Version: 2.0.6-3 Severity: important X-Debbugs-Cc: debia…@manchmal.in-ulm.de Bonjour, the latest upstream version of the file package introduced a detection of SQLite write-ahead shared memory files. As a result, the autopkgtest of nutsqlite breaks when using that version (1:5.45-1, currently in experimental). autopkgtest log: ci.debian.net/data/autopkgtest/unstable/amd64/n/nutsqlite/37303558/log.gz Please change run-unit-test | test “$(file nut.db-shm | awk…

What are some alternatives? When comparing zenstack and petstore-openapi-zenstack you can also consider the following projects: supabase-tenant-rbac – A template for implementing basic RBAC for a multi-tenant supabase project Prisma – Next-generation ORM for Node.js & TypeScript | PostgreSQL, MySQL, MariaDB, SQL Server, SQLite, MongoDB and CockroachDB vercel – Develop….

AbbVie’s Genomics Research Center Computational Genomics is looking for a highly motivated computational biologist (Senior Scientist I/II, Bioinformatics) to join a team of bioinformatics scientists investigating aging and age-related diseases. AbbVie’s GRC is a center of excellence for bioinformatics, functional genomics, and human genetics. The GRC works across all R&D…

How to download ChEBI Ontology Classes 2 I downloaded the ChEBI .sql files from here: www.ebi.ac.uk/chebi/downloadsForward.do and they have the list of compounds and relationships between compounds, but I can’t find anywhere in there the list of ontological classes. For example: Flavonoids: www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:47916 Biological roles: www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:24432 Biomarkers: www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:59163 I need…

At Cepheid, we are passionate about improving health care through fast, accurate diagnostic testing. Our mission drives us, every moment of every day, as we develop scalable, groundbreaking solutions to solve the world’s most complex health challenges. Our associates are involved in every stage of molecular diagnostics, from ideation to…

Description I am trying to start Notebook via Slurm on JupyterHub.The Slurm job is running and the Notebook is up and running, but the Hub screen still says “Cluster job Running … Waiting to connect” is still displayed on the Hub screen.It then times out and exits. Note that JupyterHub,…

Does anyone know what cmpress is? 1 Hi! I am trying to make the Trinotate boilerplate and apparently I’m missing cmpress. data/programs/Trinotate-Trinotate-v4.0.1/Trinotate –create –db myTrinotate.sqlite –trinotate_data_dir /data/programs/Trinotate-Trinotate-v4.0.1/util/databases –use_diamond which: no cmpress in path -error, cannot locate required utility: cmpress, be sure it is installed and available via your PATH env…

Is the following safe to use in a Shiny app (that might have a few concurrent users): dbExecute(pool, “BEGIN TRANSACTION;”) dbExecute(pool, “INSERT INTO cars (speed, dist) VALUES (1, 1);”) dbExecute(pool, “INSERT INTO cars (speed, dist) VALUES (3, 3);”) dbExecute(pool, “COMMIT TRANSACTION;”) It does not seem to cause any issues but…

At Cepheid, we are passionate about improving health care through fast, accurate diagnostic testing. Our mission drives us, every moment of every day, as we develop scalable, groundbreaking solutions to solve the world’s most complex health challenges. Our associates are involved in every stage of molecular diagnostics, from ideation to…

The Genomics Research Center (GRC) is a center of excellence for genetics and genomics that supports both Discovery and Development. The GRC plays an integral role towards our goal of developing extraordinary genetics and genomics research, focusing on finding the right targets and helping us better understand not only human…

AbbVie’s Genomics Research Center Computational Genomics is looking for a highly motivated computational biologist (Senior Scientist I/II, Bioinformatics) to join a team of bioinformatics scientists investigating aging and age-related diseases. AbbVie’s GRC is a center of excellence for bioinformatics, functional genomics, and human genetics. The GRC works across all R&D…

I am looking into what is required to support nanotime objects in RSQLite queries. They are just integer64 wrappers. Here is an example: con <- DBI::dbConnect(RSQLite::SQLite(), “:memory:”) ts <- nanotime::as.nanotime(Sys.time()) str(ts) # integer64 2023-06-04 17:30:21.669581000 DBI::dbGetQuery(con, ‘SELECT :ts AS x’, list(‘ts’ = ts)) # returns 5.757609e-196 tsi <- bit64::as.integer64(ts) DBI::dbGetQuery(con,…

Project Introduction: This project is going to utlize techniques our team has learned from our cloud computing class, Social Media Data Analytics Class, & EDA clasess. We are going to utilizes a corpus of text from multiple data sources and apply different topic modeling algorithms. The Data Analytical method: Simple…

A compilation of metadata from NCBI GEO Bioconductor version: 2.6 The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data of interest can be challenging using current tools. GEOmetadb is an attempt to make access to the metadata associated with samples, platforms, and…

The Genomics Research Center (GRC) is a center of excellence for genetics and genomics that supports both Discovery and Development. The GRC plays an integral role towards our goal of developing extraordinary genetics and genomics research, focusing on finding the right targets and helping us better understand not only human…

chat version: 2.0.0 hub error log [W 2023-05-11 08:27:49.529 JupyterHub app:2860] init_spawners did not complete within 10 seconds. Allowing to complete in the background. [I 2023-05-11 08:27:49.529 JupyterHub app:3057] Not starting proxy [I 2023-05-11 08:27:49.553 JupyterHub app:3093] Hub API listening on http://:8081/hub/ [I 2023-05-11 08:27:49.553 JupyterHub app:3095] Private Hub API…

Hello, I am working on the pathfinding step of the PHG pipeline and am currently trying to resolve a related issue regarding the correct parameters, described here . However when I try to rerun only the pathfinding step I run into the same error repeatedly. I have had the same…

Hi, I am getting some conflicts when I am trying to install some older version of pytorch. Using the command “conda install pytorch==1.8.0 torchvision==0.9.0 torchaudio==0.8.0 cudatoolkit=10.2 -c pytorch”. Also in the end pytorch is not getting installed. Below is what is printed on the terminal after running the above command….

minrk April 20, 2023, 12:21pm 1 JupyterHub 4.0 is out! 4.0 is a major release, but a small one. There are three major changes that should be invisible to most users: Groups can now have ‘properties’, editable via the admin page, which can be used by Spawners for their operations.This…

DOI: 10.18129/B9.bioc.AHLRBaseDbs   This is the development version of AHLRBaseDbs; for the stable release version, see AHLRBaseDbs. LRBaseDbs for AnnotationHub Bioconductor version: Development (3.17) Supplies AnnotationHub with `LRbaseDb` Ligand-Receptor annotation databases for many species. All the SQLite files are generated by our Snakemake workflow [lrbase-workflow](https://github.com/rikenbit/lrbase-workflow). For the details, see the…

Despite its recent gain in popularity, big data is still relatively uncertain compared to other established tech fields. As a result, most beginners find practicing and studying theories and concepts difficult because of a lack of data and resources. However, by using Kaggle for data science, you can overcome this…

The Genomics Research Center (GRC) is a center of excellence for genetics and genomics that supports both Discovery and Development. The GRC plays an integral role towards our goal of developing extraordinary genetics and genomics research, focusing on finding the right targets and helping us better understand not only human…

System Information Strapi Version: 4.9.0 Operating System: Windows 11 Database: sqlite Node Version: 18.15.0 NPM Version: 9.5.0 Yarn Version: 1.22.19 OpenApi generator version: typescript-fetch 6.5.0 Hiya strapi-community, I’ve added the documentation plugin to Strapi to generate OpenApi-compliant documentation. The documentation is generated and can be viewed on the Swagger documentation…

AbbVie’s Genomics Research Center Computational Genomics is looking for a highly motivated computational biologist (Senior Scientist I/II, Bioinformatics) to join a team of bioinformatics scientists investigating aging and age-related diseases. AbbVie’s GRC is a center of excellence for bioinformatics, functional genomics, and human genetics. The GRC works across all R&D…

The Center for Quantitative Genetics and Genomics (QGG) at Aarhus University invites applications for a position as Postdoc in the field of bioinformatics and sequence analysis as per 1 August 2023 or as soon as possible thereafter. Expected start date and duration of employmentThe position is a fixed-term full-time position…

I’m trying to set up a jupyterhub on my server and access it via an external network. I’m new on it so I’m using this repo as a starting point. I changed jupyterhub_config.py to use a Dummy authenticator. The complete file looks like this: import os c = get_config()  #…

From GeneSetEnrichmentAnalysisWiki GSEA Home | Downloads | Molecular Signatures Database | Documentation | Contact Introduction With the release of MSigDB 2023.1 we have created a new SQLite database for the fully annotated gene sets in both the Human (2023.1.Hs) and the Mouse (2023.1.Ms) resources. Each ships as a single-file database…

We are looking to hire a motivated Postdoc in bioinformatics and sequence analysis to join our stellar team at Aarhus Universitet in Århus C.Growing your career as a Full Time Postdoc in bioinformatics and sequence analysis is a great opportunity to develop useful skills.If you are strong in cooperation, people…

If you are a developer familiar with RESTful APIs, you might have heard of OpenAPI. It is a specification for describing RESTful APIs in a format readable for humans and machines. Building a public-facing OpenAPI includes three tasks: Authoring an OpenAPI specification which serves as the contract between the API…

I am trying to annotate a list of SNPs using the hg38 genome (knownGene) and locateVariants(). The program is able to successfully run and provide “GeneIDs” for several of the loci. However, some GeneIDs are applied to SNPs in completely different regions and on completely different chromosomes. When I cross…

Hello! I am trying to do the last few steps of the Practical Haplotype Graph pipeline as described here . I am running PHG v1.2, have loaded the Haplotypes to the database, created the pangenome fasta and am now trying to impute the best paths for different samples using WGS…

What are some alternatives? When comparing bwa-mem2 and htslib you can also consider the following projects: minimap2 – A versatile pairwise aligner for genomic and spliced nucleotide sequences bowtie2 – A fast and sensitive gapped read aligner genozip – A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF,…

I have an error in my pathing step in the PHG (version 1.3) pipeline. I have 19 taxa each with ~71,000 reference ranges, anchorwave haplotypes from assemblies, and I have been able to map short-read samples to the indexed pangenome. However, when I try to run the -imputePipeline plugin to…

Embeds the SQLite database engine in R, providing a DBI-compliant interface. SQLite is a public-domain, single-user, very light-weight database engine that implements a decent subset of the SQL 92 standard, including the core table creation, updating, insertion, and selection operations, plus transaction management. You can install the latest released version…

Video Timeline 00:00 Video Bumper00:06 Introduction00:17 Description of pre-requisites: Homebrew videoVisit http:/00:45 Go to the Spotlight search in top right00:50 Type Terminal in spotlight search to open Terminal00:59 Install the homebrew package for unixodbc01:30 Install the homebrew package for sqliteodbc02:20 View driver configuration required for the SQLite Driver on the…

Clarification on the usage of pangenomeHaplotypeMethod/pathHaplotypeMethod 0 Hello! I am currently trying to impute paths through a built Practical Haplotype Graph, i.e. use the -ImputePipelinePlugin -imputeTarget command. The PHG version I use is 1.2. I populated the database using assemblies and the built-in anchorwave plugin. I have fastq files as…

Changing Ownership Many of the files and directories mentioned in this chapter are, by default, owned by the rstudio-pm user. If you change the RunAs user for the RStudio Package Manager service, you will need to change ownership of these files and directories. See C for details on changing the…

sam123 February 8, 2023, 5:01pm 1 Hi, there, I rebuild Hub docker image based on amazon linux2. When I tried to run it locally, I got error:For the sqlite version error: sqlalchemy.exc.NotSupportedError: (sqlite3.NotSupportedError) deterministic=True requires SQLite 3.8.3 or higher The default SQLite coming with amazon linux2 is 3.7.17. However, I…

Hi there, a bit mystified with how to pass this parameter. It’s there in my config file, and seems to be read, but then eventually i get the warning that localGVCFFolder doesn’t have a parameter in the config file WARN net.maizegenetics.pangenome.pipeline.MakeInitialPHGDBPipelinePlugin – No localGVCFFolder parameter in config file – will…

Gene trans map for Trinotate input using non-Trinity assembled transcriptome? 2 I am following the Trinotate pipeline to functionally annotate an IsoSeq transcriptome for a non-model organism. I’ve performed all of the necessary TransDecoder steps and am at the stage of the Trinotate pipeline where I am loading data into…

issues with amber_minimize.py failing to use CUDA within alphafold 0 When I try and run alphafold from ubuntu command line with amber enabled, it’s throwing these errors. I0125 17:33:14.174568 47215575258112 amber_minimize.py:407] Minimizing protein, attempt 1 of 100. I0125 17:33:14.555528 47215575258112 amber_minimize.py:68] Restraining 685 / 1336 particles. I0125 17:33:14.747518 47215575258112 amber_minimize.py:417]…

Here, presented my PHG scripts, config, wgs_keyfile. 1. Create valid intervals docker run –name test_assemblies –rm -v /DATA/jysong/PHG/ver1.0_phg/:/phg/ -t maizegenetics/phg:1.0 /tassel-5-standalone/run_pipeline.pl -Xmx100G -debug -configParameters /phg/Masterconfig.txt -CreateValidIntervalsFilePlugin -intervalsFile /phg/inputDir/reference/glyma.Wm82.gnm4.ann1.T8TQ.gene_models_main.bed -referenceFasta /phg/inputDir/reference/glyma.Wm82.gnm4.4PTR.genome_main.fixed.fna.gz -mergeOverlaps true -generatedFile /phg/validBedFile.bed -endPlugin &> Log/1.Create_validinterval.txt & 2. Create initial DB docker run –name create_initial_db –rm -v /DATA/jysong/PHG/ver1.0_phg/:/phg/ -t…

Recently, in the development process, binary files need to be saved in the database, so I learned about the data type of sqlite3 and found that blob can store binary data. But what about blobs? What sentence do you use? In fact, it needs to operate some underlying APIs of…

DOI: 10.18129/B9.bioc.AHEnsDbs     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see AHEnsDbs. EnsDbs for AnnotationHub Bioconductor version: 3.10 Supplies AnnotationHub with EnsDb Ensembl-based annotation databases for all species. EnsDb SQLite databases are generated separately from Ensembl MySQL databases using functions from the…

python – OperationalError: database is locked I have made some repetitive operations in my application(testing it), and suddenly I’m getting a weird error: OperationalError: database is locked I’ve restarted the server, but the error persists.… how to close resultset in RMySQL? I…

DOI: 10.18129/B9.bioc.AHLRBaseDbs     LRBaseDbs for AnnotationHub Bioconductor version: Release (3.14) Supplies AnnotationHub with `LRbaseDb` Ligand-Receptor annotation databases for many species. All the SQLite files are generated by our Snakemake workflow [lrbase-workflow](https://github.com/rikenbit/lrbase-workflow). For the details, see the README.md of lrbase-workflow. Author: Koki Tsuyuzaki [aut, cre], Manabu Ishii [aut], Itoshi Nikaido…

I now think that the default mode should be to return an error here. That ship has sailed now. SQLite is fairly unique in its flexibility to store arbitrary data in the columns. For your use case I’d recommend segmenting by data type: library(RSQLite) con <- dbConnect(SQLite(), “:memory:”) dbGetQuery(con, “SELECT…

A simple SQLite clone in Rust. This is basically a translation of the C code present on this brilliant tutorial into Rust(not fully idiomatic). This code contains implementation only upto Part 5 in the tutorial. This a very simple database and is a small project I took up to gain…

SQLite is a file level database, hence to reference it requires a full directory path. No where do you specify the working directory or a full path in the file name. By default, R will use the current working directory contained in getwd(). If database is not contained in this…

Hi, I’m trying to learn how to use RSQLite but I’m already having a problem, wondered if anyone knows how to fix it. I have a pre-existing database (.data) file which does not have attribute names and I am trying to create a SQLite database with a table defined with…

Description Copies a database connection to a file or to another database connection. It can be used to save an in-memory database (created using dbname = “:memory:” or dbname = “file::memory:”) to a file or to create an in-memory database a copy of another database. Usage sqliteCopyDatabase(from, to) Arguments from…

You’re not using the pattern suggested by the RSQLite documentation. That documentation uses dbWriteTable to copy a data frame into a SQLite table: dbWriteTable(con, “mtcars”, mtcars) According to this documentation, your full code would look something like this: con <- dbConnect(RSQLite::SQLite(), “./mtcars.db”) data(mtcars) dbWriteTable(con, “mtcars”, mtcars) dbListTables(con) # Fetch all…

I am trying to scrape some pitchf/x data and store it in an SQLite database. However, I am receiving the following error when I run the following code: library(RSQLite) library(dplyr) db <- src_sqlite(“pitchfx.sqlite3”, create = T) This is the error: Error in h(simpleError(msg, call)) : error in evaluating the argument…

This may be a very basic question for guys who handle daily with programming issues! And until today I was not able to find the right words to ask and now I hope I can explain clearly what I want! It is technically not a coding question! It is not…

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

Platform Design Information Package Builder Bioconductor version: 2.5 Builds platform design information packages. These consist of a SQLite database containing feature-level data such as x, y position on chip and featureSet ID. The database also incorporates featureSet-level annotation data. The products of this packages are used by the oligo pkg….

tabix for ID column 4 Hello, I’m looking for something similar to tabix. But instead of looking for informations within a given region, I would like to use the values in the ID column for quickly lookup. So for example I would like to take the compressed dbSNP file, index…