Merge pull request #51 from StevenWingett/pre_release

Pre release

.github/workflows/git_actions.yml

@@ -5,9 +5,9 @@ name: CI
 # Controls when the action will run. Triggers the workflow on push or pull request
 on:
   push:
-    branches: [ master, pre_release ]
+    branches: [ master ]
   pull_request:
-    branches: [ master, pre_release ]
+    branches: [ master ]
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:

README.txt

@@ -11,7 +11,7 @@ The FastQ Screen Homepage is found at:
 https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen
 
 Full documentation on using the software is provided at:
-https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/_build/html/index.html
+https://stevenwingett.github.io/FastQ-Screen/
 
 The codebase is maintained at:
 https://github.com/StevenWingett/FastQ-Screen

RELEASE_NOTES.txt

@@ -1,3 +1,11 @@
+Release notes for FastQ Screen v0.15.2 (26 January 2022)
+--------------------------------------------------------
+Updated documentation
+
+Provided details on the genomes downloaded with the 
+command --get_genomes for possible future reference.
+
+
 Release notes for FastQ Screen v0.15.1 (11 January 2022)
 --------------------------------------------------------
 Updated contact details. 

docs/_config.yml

@@ -0,0 +1 @@
+theme: jekyll-theme-modernist

download_genomes/README.md

@@ -0,0 +1,3 @@
+This folder contains details on the downloaded regular (Bowtie2) and bisulphite genomes (Bismark/Bowtie2), should they need to be re-made / uploaded at some future date.
+
+This folder contains a tree of the files on the remote FTP, the regular/bisulphite configuration files downloaded from the FTP and the FTP location file downloaded from the Babraham server.

download_genomes/bisulfite_genomes_config_file/fastq_screen.conf

@@ -0,0 +1,106 @@
+# This is a configuration file for fastq_screen
+
+############
+## Bowtie2 #
+############
+## If the Bowtie2 binary is not in your PATH then you can 
+## set this value to tell the program where to find it.
+## Uncomment the line below and set the appropriate location
+
+#BOWTIE2	/bi/apps/bowtie2/2.3.2/bowtie2
+
+
+############
+## BISMARK #
+############
+## If the Bismark binary is not in your PATH then you can 
+## set this value to tell the program where to find it.
+## Uncomment the line below and set the appropriate location
+
+#BISMARK	/bi/apps/bismark/bismark
+
+
+############
+## Threads #
+############
+## Bowtie can be made to run across multiple CPU cores to
+## speed up your searches. Set this value to the number
+## of cores you want to use for your searches.
+
+THREADS		7
+
+##############
+## Databases #
+##############
+## This section allows you to configure multiple databases
+## to search against in your screen.  For each database
+## you need to provide a database name (which can't contain
+## spaces) and the location of the bowtie indices which 
+## you created for that database.
+## 
+## The default entries shown below are only suggested examples
+## you can add as many DATABASE sections as you like, and you
+## can comment out or remove as many of the existing entries
+## as you like.
+
+
+
+#########
+## Human - sequences available from
+## ftp://ftp.ensembl.org/pub/current/fasta/homo_sapiens/dna/
+DATABASE	Human	[FastQ_Screen_Genomes_Path]/Human/GRCh38
+
+
+
+#########
+## Mouse - sequence available from
+## ftp://ftp.ensembl.org/pub/current/fasta/mus_musculus/dna/
+DATABASE	Mouse	[FastQ_Screen_Genomes_Path]/Mouse/GRCm38
+
+
+
+#########
+## Rat - sequence available from
+## ftp://ftp.ensembl.org/pub/current/fasta/rattus_norvegicus/dna/
+DATABASE	Rat	[FastQ_Screen_Genomes_Path]/Rat/Rnor_6.0 
+
+
+
+############
+# Drosophila
+DATABASE	Drosophila	[FastQ_Screen_Genomes_Path]/Drosophila_melanogaster/BDGP6
+
+
+
+#########
+## Worm
+DATABASE	Worm	[FastQ_Screen_Genomes_Path]/C_elegans/WBcel235
+
+
+
+#########
+## Yeast - sequence available from
+## ftp://ftp.ensembl.org/pub/current/fasta/saccharomyces_cerevisiae/dna/
+DATABASE	Yeast	[FastQ_Screen_Genomes_Path]/Yeast/R64-1-1
+
+
+
+#########
+## Arabidopsis - sequences available from 
+DATABASE	Arabidopsis	     [FastQ_Screen_Genomes_Path]/Arabidopsis/TAIR10
+
+
+
+#########
+## Ecoli
+## Sequence available from EMBL accession U00096.2
+DATABASE	Ecoli	[FastQ_Screen_Genomes_Path]/E_coli/NC_010473
+
+
+
+
+########
+## PhiX - sequence available from Refseq accession NC_001422.1
+DATABASE	PhiX	     [FastQ_Screen_Genomes_Path]/PhiX/phiX174_plus_SNPs
+
+

download_genomes/genome_locations.txt

@@ -0,0 +1,2 @@
+ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes/
+ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/