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- Conocimientos básicos de Linux y su linea de comando (CLI) | - Conocimientos básicos de Linux y su linea de comando (CLI) | ||
- | ===== Herramientas ===== | + | ===== ===== |
+ | |||
+ | ===== Aplicaciones disponibles en Soroban (system) ===== | ||
+ | |||
+ | Compiladores, interpretes, librerias, y utilidades | ||
+ | |||
+ | ---- | ||
+ | |||
+ | índice : A|B|C|D|E|F|G|H|I|J|K|L|M|N|[[:o|O]]|P|Q|R|S|T|U|V|W|X|Y|Z | ||
+ | |||
+ | ---- | ||
+ | |||
+ | ^ ^Software^Versión^Descripción| | ||
+ | |**A** | | | | | ||
+ | | |Anaconda python|3.7.8|Interprete python optimizado| | ||
+ | |**B** | | | | | ||
+ | |**C** |cmake|3.15.4|Utilidad para compilar en Linux| | ||
+ | |**D** | | | | | ||
+ | |**E** | | | | | ||
+ | |**F** | | | | | ||
+ | |**G** | | | | | ||
+ | | |GCC|8.3.1|Compilador c/c++/fortran| | ||
+ | | |GCC|5.5.5|Compilador c/c++/fortran| | ||
+ | | |Go|1.15.2|Compilador de Lenguaje GO| | ||
+ | | |Clang|3.4.2|Compilador c/c++ de LLVM| | ||
+ | |**H** | | | | | ||
+ | | |HDF5|1.10.5|FileSystem Distribuido| | ||
+ | |**I** | | | | | ||
+ | |**J** | | | | | ||
+ | | |Java Develop Kit (JDK)|11.0.8|JDK (openjdk) librerias/compilador JAVA| | ||
+ | |**K** | | | | | ||
+ | |**L** | | | | | ||
+ | |**M** | | | | | ||
+ | | |Math Kernel Library (MKL)|2018.4-274|Librerias matemáticas optimizadas de Intel| | ||
+ | |**N** | | | | | ||
+ | |**O** | | | | | ||
+ | | |openmpi|1.10.7|Programación paralela| | ||
+ | | |openmpi|3.1.5|Programación paralela| | ||
+ | | |openmpi|1.6.5|Programación paralela| | ||
+ | | |openmpi|2.1.6|Programación paralela| | ||
+ | | |openblas|3.3-2|Implementación opensource de BLAS y LAPACK ; algebra lineal| | ||
+ | |**P** | | | | | ||
+ | | |Perl|5.16.3|Interprete del lenguaje Perl| | ||
+ | |**Q** | | | | | ||
+ | |**R** | | | | | ||
+ | |**S** | | | | | ||
+ | |**T** | | | | | ||
+ | |**U** | | | | | ||
+ | |**V** | | | | | ||
+ | |**W** | | | | | ||
+ | |**X** | | | | | ||
+ | |**Y** | | | | | ||
+ | |**Z** | | | | | ||
+ | |||
+ | ====== Aplicaciones Científicas ====== | ||
+ | |||
+ | Bioinformatics, Chemistry, Physics, etc | ||
+ | |||
+ | índice : A|B|C|D|E|F|G|H|I|J|K|L|M|N|O|P|Q|R|S|T|U|W|X|Y|Z | ||
+ | |||
+ | ---- | ||
+ | |||
+ | | \\ **#** | \\ **Aplicación** | \\ **Versión** | \\ **Descripción** | | ||
+ | |**A** | | | | | ||
+ | | |aragorn|1.2.38|tRNA (and tmRNA) detection| | ||
+ | | |arb|6.0.6|Phylogenetic analysis of rRNA and other biological sequences such as amino acids| | ||
+ | | |ascp|3.9.9|–| | ||
+ | |**B** | | | | | ||
+ | | |bowtie2|0.7.17|software package for mapping low-divergent sequences against a large reference genome, such as the human genome| | ||
+ | | |bwa|2.4.1|alineación de secuencias y el análisis de secuencias en bioinformática| | ||
+ | | |blast+|2.9.0|Alineamiento de secuencias de tipo local, ya sea de ADN, ARN o de proteínas| | ||
+ | | |blast+|2.10.0(default)|Alineamiento de secuencias de tipo local, ya sea de ADN, ARN o de proteínas| | ||
+ | | |blast|2.2.26|Alineamiento de secuencias de tipo local, ya sea de ADN, ARN o de proteínas| | ||
+ | | |bedtools|2.29.2|swiss-army knife of tools for a wide-range of genomics analysis tasks| | ||
+ | | |bedops|2.4.38|highly scalable and easily-parallelizable genome analysis toolkit| | ||
+ | | |beagle-lib|3.1.2|high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics| | ||
+ | | |bcftools|1.10.2|set of utilities that manipulate variant calls| | ||
+ | | |bbtools|38.86|suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data| | ||
+ | | |barrnap|0.9|predicts the location of ribosomal RNA genes in genomes| | ||
+ | | |bamtools|2.5.1|toolkit for handling BAM files.| | ||
+ | | | | | | | ||
+ | |**C** | | | | | ||
+ | | |cufflinks|2.10|finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads| | ||
+ | | |circos|2.2.1|Transcriptome assembly and differential expression analysis for RNA-Seq.| | ||
+ | | |cutadapt|0.69-9|for visualizing data and information. It visualizes data in a circular layout| | ||
+ | | |checkm|1.1.2|set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes| | ||
+ | | |cdhit|4.8.1|Takes a fasta format sequence database as input and produces a set of 'non-redundant' (nr)…| | ||
+ | | |canu|1.9|Fork of the Celera Assembler designed for high-noise single-molecule sequencing| | ||
+ | | | | | | | ||
+ | | | | | | | ||
+ | |**D** | | | | | ||
+ | | |diamond|0.9.35|molecular and crystal structure visualization software| | ||
+ | |**E** | | | | | ||
+ | |**F** | | | | | ||
+ | |**G** | | | | | ||
+ | | |gromacs|2019.4|Modelamiento Molecular| | ||
+ | |**H** | | | | | ||
+ | | |hmmer|2.3.2|biosequence analysis using profile hidden Markov models .| | ||
+ | | |hmmer|3.1b1|biosequence analysis using profile hidden Markov models .| | ||
+ | | |hmmer|3.1b2|biosequence analysis using profile hidden Markov models .| | ||
+ | | |hmmer|3.2.1|biosequence analysis using profile hidden Markov models .| | ||
+ | | | | | | | ||
+ | |**I** | | | | | ||
+ | |**J** | | | | | ||
+ | |**K** | | | | | ||
+ | |**L** | | | | | ||
+ | |**M** | | | | | ||
+ | |**N** | | | | | ||
+ | | |Namd2|2019-11-27-multicore|Modelamiento Molecular| | ||
+ | |**P** | | | | | ||
+ | |**Q** | | | | | ||
+ | |**R** | | | | | ||
+ | | |R|3.6.1|Analísis Estadistico| | ||
+ | | | | | | | ||
+ | |**W** | | | | | ||
+ | | |WRF|3.9.1|Mesoscale numerical weather prediction| | ||
+ | | |WRF|4.0|Mesoscale numerical weather prediction| | ||
+ | |**X** | | | | | ||
+ | | \\ **6** | \\ netcdf/c| \\ 4.7.3| \\ Network Common Data Form| | ||
+ | | \\ **7** | \\ netcdf/fortran| \\ 4.5.2| \\ Network Common Data Form| | ||
+ | | \\ **8** | \\ quantum-espresso/schrodinger| \\ 6.4.1-2019-4| \\ Modelamiento Molecular| | ||
+ | | \\ **32** | \\ eggnog-mapper| \\ 2.0.1| \\ tool for functional annotation of large sets of sequences based on fast orthology assignments using precomputed clusters| | ||
+ | | \\ **33** | \\ EMBOSS| \\ 6.6.0| \\ European Molecular Biology Open Software Suite| | ||
+ | | \\ **34** | \\ FastANI| \\ 1.3| \\ Produces accurate ANI estimates and is faster than alignment (e.g., BLAST)- based approaches.| | ||
+ | | \\ **35** | \\ vcftools| \\ 0.1.17| \\ package designed for working with VCF files| | ||
+ | | \\ **36** | \\ Unicycler| \\ 0.4.9b| \\ assembly pipeline for bacterial genomes| | ||
+ | | \\ **37** | \\ tRNAscan-SE| \\ 2.0.5| \\ searches for tRNA genes in genomic sequences| | ||
+ | | \\ **38** | \\ trinityrnaseq| \\ 2.11.0| \\ Trinity RNA-Seq de novo transcriptome assembly| | ||
+ | | \\ **39** | \\ trf| \\ 4.09| \\ Analyze DNA sequences| | ||
+ | | \\ **40** | \\ TransDecoder| \\ 5.5.0| \\ Assist in the identification of potential coding regions within ….| | ||
+ | | \\ **41** | \\ tophat| \\ 2.1.1| \\ Alineación del rendimiento de las lecturas de secuenciación de cDNA …| | ||
+ | | \\ **42** | \\ tbl2asn| \\ 3.10.0| \\ Automates the creation of sequence records for submission to GenBank| | ||
+ | | \\ **43** | \\ ssu-align| \\ 0.1.1| \\ identifying, aligning, masking and visualizing archaeal 16S, bacterial 16S and eukaryotic 18S…| | ||
+ | | \\ **44** | \\ sratoolkit| \\ 2.10.7| \\ Using the SRA Toolkit to convert .sra files into other formats …| | ||
+ | | \\ **45** | \\ SPAdes| \\ 3.14.1| \\ Assembly toolkit containing various assembly pipelines.| | ||
+ | | \\ **46** | \\ SPAdes| \\ 3.13.2| \\ Assembly toolkit containing various assembly pipelines.| | ||
+ | | \\ **47** | \\ SINA| \\ 1.6.1| \\ accurate high-throughput multiple sequence alignment of ribosomal RNA genes.| | ||
+ | | \\ **48** | \\ seqtk| \\ 1.3| \\ A fast and lightweight tool for processing sequences in the FASTA or FASTQ format.| | ||
+ | | \\ **49** | \\ seqkit| \\ 0.12.1| \\ Seqkit is a tool for manipulating fasta and fastq files.| | ||
+ | | \\ **50** | \\ samtools| \\ 1.10.2| \\ suite of programs for interacting with high-throughput sequencing data| | ||
+ | | \\ **51** | \\ salmon| \\ 1.2.1| \\ Is a tool for quantifying the expression of transcripts using RNA-seq data.| | ||
+ | | \\ **52** | \\ RSEM| \\ 1.3.3| \\ Tool for the quantification of RNA-seq data.| | ||
+ | | \\ **53** | \\ roary| \\ 1.7.7| \\ Application for rapidly constructing pan genomes from large numbers of prokaryote sample| | ||
+ | | \\ **54** | \\ racon| \\ 1.4.16| \\ Consensus sequence| | ||
+ | | \\ **55** | \\ quast| \\ 5.1.0rc1| \\ Quality Assessment Tool for Genome Assemblies| | ||
+ | | \\ **56** | \\ pyani| \\ 0.2.10| \\ a Python3 module that provides support for calculating average nucleotide identity (ANI)| | ||
+ | | \\ **57** | \\ prokka| \\ 1.14.6| \\ tool for the rapid annotation of prokaryotic genomes| | ||
+ | | \\ **58** | \\ prodigal| \\ 2.6.3| \\ Prodigal is an unsupervised machine learning algorithm| | ||
+ | | \\ **59** | \\ prinseq| \\ 0.20.4| \\ Tool that generates summary statistics of sequence and quality data and that is used to filter, reformat and trim …| | ||
+ | | \\ **60** | \\ prank| \\ 170427| \\ Is a probabilistic multiple alignment program for DNA,| | ||
+ | | \\ **61** | \\ pplacer| \\ 1.1.alpha17| \\ Places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference …| | ||
+ | | \\ **62** | \\ htslib| \\ 1.10.2| \\ An implementation of a unified C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data, …| | ||
+ | | \\ **63** | \\ mash| \\ 2.2| \\ Reduces large sequences and sequence sets to small, …| | ||
+ | | \\ **64** | \\ mafft| \\ 7.470| \\ is a multiple sequence alignment program for unix-like operating systems| | ||
+ | | \\ **65** | \\ ksnp| \\ 3.1.2| \\ Finds single nucleotide polymorphisms (SNPs) in whole genome data.| | ||
+ | | \\ **66** | \\ krona| \\ 2.7.1| \\ powerful metagenomic visualization tool| | ||
+ | | \\ **67** | \\ kaiju| \\ 1.7.3| \\ program for the taxonomic classification of high-throughput sequencing reads.| | ||
+ | | \\ **68** | \\ jellyfish| \\ 2.3.0| \\ tool for fast, memory-efficient counting of k-mers in DNA.| | ||
+ | | \\ **69** | \\ jdk| \\ 8.0_41| \\ Java Develop ToolKit| | ||
+ | | \\ **70** | \\ jdk| \\ 14.0.1| \\ Java Develop ToolKit| | ||
+ | | \\ **71** | \\ jdk| \\ 11.28| \\ Java Develop ToolKit| | ||
+ | | \\ **72** | \\ infernal| \\ 1.1.3| \\ for searching DNA sequence databases for RNA structure and sequence similarities| | ||
+ | | \\ **73** | \\ pilon| \\ 1.23| \\ an automated genome assembly improvement and variant detection tool| | ||
+ | | \\ **74** | \\ picard| \\ 2.23.1| \\ a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.| | ||
+ | | \\ **75** | \\ phyml| \\ 3.3.20190909| \\ is a phylogeny software based on the maximum-likelihood principle| | ||
+ | | \\ **76** | \\ phylip| \\ 3.697| \\ a free package of programs for inferring phylogenies| | ||
+ | | \\ **77** | \\ parallel| \\ 20200622| \\ Parallel is an indispensible tool for speeding up bioinformatics. It allows you to easily parallelize commands| | ||
+ | | \\ **78** | \\ paml| \\ 4.9| \\ a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.| | ||
+ | | \\ **79** | \\ ncftp| \\ 3.2.6| \\ cliente ftp| | ||
+ | | \\ **80** | \\ muscle| \\ 3.8.31| \\ A program to create multiple sequence alignments of a large number of sequences| | ||
+ | | \\ **81** | \\ MUMmer| \\ 3.23| \\ an open source software package for the rapid alignment of very large DNA and amino acid sequences| | ||
+ | | \\ **82** | \\ mothur| \\ 1.44.1| \\ a single resource to analyze molecular data that is used by microbial ecologists| | ||
+ | | \\ **83** | \\ minimap2| \\ 2.17| \\ pairwise alignment for nucleotide sequences.| | ||
+ | | \\ **84** | \\ miniconda| \\ 4.8.3| \\ python minimalist| | ||
+ | | \\ **85** | \\ MCL| \\ 14-137| \\ a cluster algorithm for graphs| | ||
+ | | \\ **86** | \\ MinCED| \\ 0.4.2| \\ program to find Clustered Regularly Interspaced Short .| | ||
+ | | \\ **87** | \\ fastqc| \\ 0.11.9| \\ a quality control application for high throughput sequence data.| | ||
+ | | \\ **88** | \\ fasttree| \\ 2.1.11| \\ FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences| | ||
+ | | \\ **89** | \\ Gblocks| \\ 0.91b| \\ computer program written in ANSI C language that eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein| | ||
+ | | \\ **90** | \\ go| \\ 1.14.4| \\ compilador de lenguaje GO| | ||
+ | | \\ **91** | \\ gtdbtk| \\ 1.2.0| \\ a toolkit to classify genomes with the Genome Taxonomy Database, B| | ||
====== Activación de MFA (opcional) ====== | ====== Activación de MFA (opcional) ====== | ||
- | <font 16px/inherit;;inherit;;inherit>Multi Factor Authenticator (MFA) . Este método agrega un capa de seguridad extra a las cuentas de los investigadores, y es obligatorio para todos los usuarios.</font> | + | <font 16px/inherit;;inherit;;inherit>Multi Factor Authenticator (MFA) . Este método agrega un capa de seguridad extra a las cuentas de los investigadores, <del>y es obligatorio para todos los usuarios.</del></font> |
<font 16px/inherit;;inherit;;inherit>Para activar y usar MFA es necesario seguir tres simples pasos descritos a continuación:</font> | <font 16px/inherit;;inherit;;inherit>Para activar y usar MFA es necesario seguir tres simples pasos descritos a continuación:</font> | ||
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<font 16px/inherit;;inherit;;inherit>En situaciones especiales como perdida, daño, desinstalación o simplemente cambio de smartphone estan disponibles varias alternativas:</font> | <font 16px/inherit;;inherit;;inherit>En situaciones especiales como perdida, daño, desinstalación o simplemente cambio de smartphone estan disponibles varias alternativas:</font> | ||
- | - <font 16px/inherit;;inherit;;inherit>Utilizar uno de los 5 códigos de emergencias descritos en el paso 3 para accesar cuando google authenticator no este disponible. Eliminar el archivo .google_authenticator en tu cuenta en Soroban ejecutando el siguiente comando: rm -rf .google_authenticator , y luego repetir el paso 3.</font>- - <font 16px/inherit;;inherit;;inherit>Ingresar el actual secret key directamente en la nueva instalación de google authenticator en el smartphone para volver activar MFA.</font>- - <font 16px/inherit;;inherit;;inherit>Contactar como último recurso al siguiente correo en cualquier horario para soporte : raphael.verdugo@ufrontera.cl</font> | + | - <font 16px/inherit;;inherit;;inherit>Utilizar uno de los 5 códigos de emergencias descritos en el paso 3 para accesar cuando google authenticator no este disponible. Eliminar el archivo .google_authenticator en tu cuenta en Soroban ejecutando el siguiente comando: rm -rf .google_authenticator , y luego repetir el paso 3.</font>- |
+ | - - <font 16px/inherit;;inherit;;inherit>Ingresar el actual secret key directamente en la nueva instalación de google authenticator en el smartphone para volver activar MFA.</font>- - | ||
+ | - <font 16px/inherit;;inherit;;inherit>Contactar como último recurso al siguiente correo en cualquier horario para soporte : raphael.verdugo@ufrontera.cl</font> | ||
+ | ====== ====== | ||
+ | |||
+ | ====== Primeros pasos en Soroban ====== | ||
+ | |||
+ | [[:namespace:iniciar_session_en_soroban|iniciar session en Soroban]] | ||
+ | |||
+ | [[:namespace:cargar_un_software_en_soroban|Cargar un software en Soroban]] | ||
+ | |||
+ | [[:namespace:ejecutar_un_trabajo_en_soroban|Ejecutar un trabajo en Soroban]] | ||
+ | |||
+ | ====== Cargando un software/libreria en Soroban ====== | ||
====== Utilización de module ====== | ====== Utilización de module ====== | ||
Line 198: | Line 392: | ||
<font 16px/inherit;;inherit;;inherit>El ejemplo contiene los comandos necesarios para :</font> | <font 16px/inherit;;inherit;;inherit>El ejemplo contiene los comandos necesarios para :</font> | ||
- | - <font 16px/inherit;;inherit;;inherit>Listar las aplicaciones disponibles</font>- <font 16px/inherit;;inherit;;inherit>Cargar los programas/librerias deseados</font>- <font 16px/inherit;;inherit;;inherit>Verificar que este disponible la libreria/aplicación que se ha cargado</font>- <font 16px/inherit;;inherit;;inherit>Descargar las aplicaciones cuando no sean necesarias o se desee otra versión.</font> | + | - Listar las aplicaciones disponibles. |
+ | - Cargar los programas/librerias deseados. | ||
+ | - Verificar que este disponible la libreria/aplicación que se ha cargado. | ||
+ | - Descargar las aplicaciones cuando no sean necesarias o se desee otra versión. | ||
- | {{:namespace:module4-c.png?nolink&1500x679}} | + | - {{:namespace:module4-c.png?nolink&1500x679}} |
====== ====== | ====== ====== | ||
- | ====== ====== | + | ---- |
====== Ejecutar un trabajo sin SLURM ====== | ====== Ejecutar un trabajo sin SLURM ====== | ||
- | ====== Ejecutar una simulación con screen ====== | + | ===== Ejecutar una simulación con screen ===== |
(**multiplexor screen)** | (**multiplexor screen)** |