How to Uninstall Roche 454 Data Analysis, Data Processing v2.8 @ CentOS Linux 5.x ?

roche

I’m trying uninstall via rpm package managment and works for me :),
following my instructions you could downgrade software versions :)

you will need to list all roche 454 software installed via rpm (main setup.sh )

[jacob]$ rpm -q –all | grep gs

gsMapper-2.8-1
gsNewbler-2.8-1
gsRunProcessor-2.8-1
gsRunProcessorManager-2.6-1
gsSeqTools-2.8-1
gsAmplicons-2.8-1

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VCF Lib – for parsing and manipulating VCF files FIXED

vcfliblogo

like Erik said in his github vcf lib project:

The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended to concisely describe reference-indexed variations between individuals. The current specification can be found on the 1000 Genomes wiki (http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41)

VCFLib is a simple C++ library for parsing and manipulating VCF files, + many command-line utilities

In pasts weeks I was trying to install VCFLib our HPC Cluster Computer but I had some problems to compile it , I fixed it , follow instructions below

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SOLiD2FASTQ ¿Cómo convertir ColorSpace/Qual a FASTQ?

Un problema al que te enfrentas muy seguido es como generar un archivo FASTQ a partir de tus secuencias en colores (*.csfasta) y valores de calidad (*.qual) resultado de la secuenciación por ligación de la serie de instrumentos SOLiD de la conocida empresa LifeTechnologies/AB. Vamos directo al grano sin hacer mucho alarde , de igual…

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Velvet Sequence assembler for very short reads + OpenMP

OpenMP allows a program to make use of multiple CPU cores on the same machine. I will try to use Velvet Assembler with OpenMP support. Step 1. Check if you have OpenMP enabled in your computer. Copy following C source code #include <omp.h> #include <stdio.h> int main() { #pragma omp parallel printf(“Hello from thread %d,…

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unofficial patch XSQ Tools/Linux Mint 12 Lisa

Hi guys , I’m still alive .. I developed simple patch for Life Technologies/Applied Biosystems XSQ Tools. This patch allows to run XSQ Tools in Debian based linux distributions like Linux Mint 12 or Ubuntu Linux 1. Download XSQ Tools from official website. 2. Decompress tar file $ tar -zxvf XSQ_Tools_20120109.tgz 3. Download patch tar…

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EBI Wise 2 plus updated SQUID available.

The Wise2 package is entirely open source licensed for use by both commerical and academic sites. This means that anyone can modify and
redistribute the source code without restriction. However, the use of the source code as part of a larger, and potentially propietary package depends on which portions of the source code you wish to use. Each directory has a seperate LICENSE or GNULICENSE file which you
should read, but the gist is given below.

Download updated EBI Wise 2 from here

Download from EBI (outdated version)

Installation instructions here or INSTALL

Currently I’m packaging (deb and rpm) EBI Wise 2 binaries for Debian and Red Hat based linux distros.

Jacob

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[Fixed] EBI Wise 2 runs on Linux Mint 12 Lisa

I fixed SQUID C library for EBI Wise2 bioinformatics software application.

Wise 2 was developed in C by Ewan Birney. EBI Wise 2 software compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.

I will explain step by step how to fix SQUID and install Wise 2 in your current Linux Mint “Lisa” OS (aka Ubuntu)

$ mv sqio.c sqio.c.bk

3. try to search getline string and replace it using getlineSeq string

$ sed ‘s/getline/getlineSeq/g’ sqio.c.bk > sqio.c

4. try to test using grep command

$ grep -n “getline” sqio.c

check output

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Mi Minuta Talleres Bioinformática Ciencias Genomicas UNAM 2012

Gracias a la invitación de Jerome Verleyne y Romualdo Zayas la cual agradezco mucho, participe como ponente en los talleres internacionales de bioinformática 2012 los cuales se llevaron a cabo en el Centro de Ciencias Genomicas de la UNAM del 16 al 27 de enero de 2012.

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my simple Galaxy script

Al trabajar con Galaxy y empezar a “indexar” los genomas de referencia para distintas herramientas NGS , me vi en la necesidad, en el caso de Blast, de complementar usando bash un script en python que permite preparar una base de datos para Blast en el formato adecuado para Galaxy.

Basicamente el flujo es:

Fasta File (in) – - > set_galaxy_blastdb.sh (process) – - > Galaxy Fasta File (out) – - > Blast Reference Seq

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xsq-tools on CentOS Linux 6

Follow this unofficial tutorial step by step to run xsq-tools on CentOS Linux 6 and OpenSuse Linux

1. If you are using CentOS Linux 6, OpenSuse Linux check which GNU LIBC version you have installed. you can use this command

[jacob@localhost xsq-tools]$ ldd – -version
ldd (GNU libc) 2.12

Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Written by Roland McGrath and Ulrich Drepper.

to run xsq-tools you will need GNU libc version 2.5+ !!

2. Get Official xsq-tools software package distribution from LifeTech/ABI

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Talleres Internacionales de Bioinformática / International Workshops on Bioinformatics – 2012



Nos es grato informarle que el Nodo Nacional de Bioinformática
(NNB-UNAM) y la Sociedad Iberoamericana de Bioinformática (SOIBio), con
el apoyo del Centro de Ciencias Genómicas (CCG-UNAM), el Instituto de
Biotecnología (IBt-UNAM), la Licenciatura en Ciencias Genómicas
(LCG-UNAM) y EMBnet organizan los Talleres Internacionales de
Bioinformática - 2012, que se llevarán a cabo del 16 al 27 de enero de
2012 en las instalaciones del CCG en Cuernavaca Morelos, México.

En la semana del 16 al 20 de Enero se impartirán 2 talleres de nivel
básico dirigido a principiantes en el área. En la semana del 23 al 27 de
Enero se ofrecerán 2 talleres especializados, uno dirigido a gente
trabajando en análisis de datos generados por secuenciadores de nueva
generación y otro para Administradores de Sistemas.

Para los detalles de los programas y procedimiento de registro, favor de
visitar el sitio web del evento:

http://congresos.nnb.unam.mx

Comité Organizador
TIB -2012
---------------------------
We are pleased to announce that the National Node of Bioinformatics
(NNB-UNAM) and the Iberoamerican Society of Bioinformatics (SOIBio),
with support from the Center for Genomic Sciences (CCG-UNAM), the
Institute of Biotechnology (IBT-UNAM), the Undergraduate Program in
Genomics Sciences (LCG-UNAM) and the EMBnet, organize the “International
Workshops on Bioinformatics – 2012” which will be held from January 16th
to 27th, 2012 in the CCG facilities in Cuernavaca Morelos, Mexico.

Two Basic or introductory workshops will be offered during the first
week (January 16th-20th), geared towards beginners in the field. Two
advanced workshops will be offered during the second week (January 23rd
to 27th), one designed for people working with data generated by next
generation sequencers, and the other for System Administrators.

For the details on the programs and registration procedure, please visit
the event website:

http://congresos.nnb.unam.mx

Organizing Committee
IWB - 2012

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BioScope: validar genomas de referencia

Comentando con Leonardo Varuzza , le decía que el plugin de ma.to.bam de BioScope generaba un error y aunque nuestro mapeo a nuestra referencia era correcto y completo , nuestro formato bam no se generaba y por ende cualquier otro tipo de análisis que dependiera de este formato ya no seria viable. Pues una sugerencia…

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