| (use-modules (guix packages) | |
| (guix download) | |
| (gnu packages ruby) | |
| (guix licenses) | |
| (guix build-system ruby)) | |
| (define ruby-httparty | |
| (package | |
| (name "ruby-httparty") | |
| (version "0.13.7") |
| Mar-14 07:26:36.530 [main] DEBUG nextflow.cli.Launcher - $> /usr/local/bin/nextflow run -process.executor ignite -with-timeline timeline.html . | |
| Mar-14 07:26:36.645 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 0.17.3 | |
| Mar-14 07:26:36.910 [main] INFO nextflow.cli.CmdRun - Launching ./main.nf | |
| Mar-14 07:26:37.549 [main] DEBUG nextflow.Session - Session uuid: f25aca13-5ab7-45f6-9d3a-6fe5a5cf738a | |
| Mar-14 07:26:37.555 [main] DEBUG nextflow.Session - Executor pool size: 2 | |
| Mar-14 07:26:37.576 [main] DEBUG nextflow.cli.CmdRun - | |
| Version: 0.17.3 build 3495 | |
| Modified: 18-02-2016 11:00 UTC | |
| System: Linux 4.2.0-25-generic | |
| Runtime: Groovy 2.4.5 on OpenJDK 64-Bit Server VM 1.8.0_66-internal-b17 |
| (define-public codingquarry | |
| (package | |
| (name "codingquarry") | |
| (version "2.0") | |
| (source (origin | |
| (method url-fetch) | |
| (uri (string-append | |
| "mirror://sourceforge/codingquarry/CodingQuarry_v" | |
| version ".tar.gz")) | |
| (sha256 |
| #!/usr/bin/env ruby | |
| require 'nokogiri' | |
| require 'optparse' | |
| require 'pathname' | |
| require 'tempfile' | |
| require 'ostruct' | |
| require 'digest' | |
| require 'logger' | |
| require 'tmpdir' |
| #!/usr/bin/env nextflow | |
| params.species = 'species.txt' | |
| species_names = Channel.fromPath(params.species) | |
| genomes = Channel.fromPath(params.genomes).map{ file -> [file.name.lastIndexOf('.').with {it != -1 ? file.name[0..<it] : file.name}, file] }.distinct { id, file -> id } | |
| process get_dothideomycete_descriptions { | |
| output: | |
| file('assemblies.json') into ascomycete_assemblies_json |
=Slightly Safer Button Emergency Room=
Thanks to /u/BlueBlond for supplying the button. If you'd rather not trust that BlueBlond won't update the script to auto-click the button without your permission, this script offers a slightly safer option. The link is hard-coded to a specific version of the script in gist.
Link
| /pbstore/groupfs/Curtin/bio-sci-02/WIP/PacBio-pea_pathogens.tar.gz | |
| /pbstore/groupfs/Curtin/bio-sci-02/WIP/Af_1_new.tar.gz | |
| /pbstore/groupfs/Curtin/bio-sci-02/A_rabiei/Ar_me14/me14_RNA/me14_all_RNA_reads1.fa.tar.gz | |
| /pbstore/groupfs/Curtin/bio-sci-02/A_rabiei/Ar_me14/me14_RNA/me14_all_RNA_reads2.fa.tar.gz | |
| /pbstore/groupfs/Curtin/bio-sci-02/A_rabiei/Ar_me14/me14_RNA/trinity_Ar_me14_all_mink10_mcon150.tar.gz | |
| /pbstore/groupfs/Curtin/bio-sci-02/A_rabiei/Ar_me14/me14_RNA/th2_me14v3_all.tar.gz | |
| /pbstore/groupfs/Curtin/bio-sci-02/A_rabiei/Ar_me14/Ar_me14_v3assembly_140325/EVM_protein_analysis/me14_secretome_analysis.tar.gz | |
| /pbstore/groupfs/Curtin/bio-sci-02/A_rabiei/Ar_me14/Ar_me14_v3assembly_140325/EVM_protein_analysis/me14_Pfam.tar.gz | |
| /pbstore/groupfs/Curtin/bio-sci-02/A_lentis/Al_4/tRNA.tar.gz | |
| /pbstore/groupfs/Curtin/bio-sci-02/A_lentis/Al_4/EVM_AL4.tar.gz |
| library(devtools) | |
| #install_github("ropensci/rentrez") | |
| library(rentrez) | |
| library(tidyr) | |
| library(ggplot2) | |
| papers_by_year <- function(years, search_term){ | |
| return(sapply(years, function(y) entrez_search(db="pubmed",term=paste('(', search_term, '[Title/Abstract]) AND ("Molecular plant-microbe interactions : MPMI"[Journal] OR ""[Journal] OR "Fungal genetics and biology : FG & B"[Journal])', sep = ""), mindate=y, maxdate=y, retmax=0)$count)) | |
| } |
| FROM ubuntu:14.04 | |
| MAINTAINER Robert Syme <robsyme@gmail.com> | |
| RUN sed 's/main$/main universe/' -i /etc/apt/sources.list | |
| ENV DEBIAN_FRONTEND noninteractive | |
| RUN apt-get update -qq | |
| RUN apt-get upgrade -qqy | |
| # Get wget | |
| RUN apt-get install -qqy wget |