further scrub flexbar

griffithlab · Nov 15, 2023 · 8548f3e · 8548f3e
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diff --git a/_posts/0000-10-01-Installation.md b/_posts/0000-10-01-Installation.md
@@ -14,7 +14,7 @@ date: 0000-10-01
 First, make sure your [environment](https://rnabio.org/module-00-setup/0000/07/01/Environment/) is set up correctly.
 
 ***
-Tools needed for this analysis are: samtools, bam-readcount, HISAT2, stringtie, gffcompare, htseq-count, gtf_to_fasta (TopHat), kallisto, FastQC, Fastp, MultiQC, Picard, flexbar, Regtools, RSeqQC, bedops, gtfToGenePred, genePredToBed, how_are_we_stranded_here, CellRanger, R, BioConductor, ballgown, and other R packages. In the following installation example, the installs are local and will work whether you have root (i.e. admin) access or not. However, if root is available some binaries can/will be copied to system-wide locations (e.g., ~/bin/).
+Tools needed for this analysis are: samtools, bam-readcount, HISAT2, stringtie, gffcompare, htseq-count, gtf_to_fasta (TopHat), kallisto, FastQC, Fastp, MultiQC, Picard, Regtools, RSeqQC, bedops, gtfToGenePred, genePredToBed, how_are_we_stranded_here, CellRanger, R, BioConductor, ballgown, and other R packages. In the following installation example, the installs are local and will work whether you have root (i.e. admin) access or not. However, if root is available some binaries can/will be copied to system-wide locations (e.g., ~/bin/).
 
 Set up tool installation location:
 
@@ -191,19 +191,6 @@ wget https://github.com/broadinstitute/picard/releases/download/2.26.4/picard.ja
 java -jar $RNA_HOME/student_tools/picard.jar
 ```
 
-## [Flexbar](https://github.com/seqan/flexbar)
-
-Installation type: download precompiled binary. Citation: [PMID: 24832523](https://pubmed.ncbi.nlm.nih.gov/24832523/).
-
-```bash
-cd $RNA_HOME/student_tools/
-wget https://github.com/seqan/flexbar/releases/download/v3.5.0/flexbar-3.5.0-linux.tar.gz
-tar -xzvf flexbar-3.5.0-linux.tar.gz
-cd flexbar-3.5.0-linux/
-export LD_LIBRARY_PATH=$RNA_HOME/student_tools/flexbar-3.5.0-linux:$LD_LIBRARY_PATH
-./flexbar
-```
-
 ## [RegTools](https://github.com/griffithlab/regtools#regtools)
 
 Installation type: compile from source code using `cmake` and `make`. Citation: [bioRXiv: 10.1101/436634v2](https://www.biorxiv.org/content/10.1101/436634v2).
@@ -383,11 +370,10 @@ Solution: When you are ready you can check your approach against the [Solutions]
 To use the locally installed version of each tool without having to specify complete paths, you could add the install directory of each tool to your '$PATH' variable and set some other environment variables:
 
 ```bash
-PATH=$RNA_HOME/student_tools/genePredToBed:$RNA_HOME/student_tools/gtfToGenePred:$RNA_HOME/student_tools/bedops_linux_x86_64-v2.4.41/bin:$RNA_HOME/student_tools/samtools-1.18:$RNA_HOME/student_tools/bam-readcount/bin:$RNA_HOME/student_tools/hisat2-2.2.1:$RNA_HOME/student_tools/stringtie-2.2.1:$RNA_HOME/student_tools/gffcompare-0.12.6.Linux_x86_64:$RNA_HOME/student_tools/tophat-2.1.1.Linux_x86_64:$RNA_HOME/student_tools/kallisto_linux-v0.44.0:$RNA_HOME/student_tools/FastQC:$RNA_HOME/student_tools/fastp:$RNA_HOME/student_tools/flexbar-3.5.0-linux:$RNA_HOME/student_tools/regtools/build:/home/ubuntu/bin/bedtools2/bin:/home/ubuntu/.local/bin:$PATH
+PATH=$RNA_HOME/student_tools/genePredToBed:$RNA_HOME/student_tools/gtfToGenePred:$RNA_HOME/student_tools/bedops_linux_x86_64-v2.4.41/bin:$RNA_HOME/student_tools/samtools-1.18:$RNA_HOME/student_tools/bam-readcount/bin:$RNA_HOME/student_tools/hisat2-2.2.1:$RNA_HOME/student_tools/stringtie-2.2.1:$RNA_HOME/student_tools/gffcompare-0.12.6.Linux_x86_64:$RNA_HOME/student_tools/tophat-2.1.1.Linux_x86_64:$RNA_HOME/student_tools/kallisto_linux-v0.44.0:$RNA_HOME/student_tools/FastQC:$RNA_HOME/student_tools/fastp:$RNA_HOME/student_tools/regtools/build:/home/ubuntu/bin/bedtools2/bin:/home/ubuntu/.local/bin:$PATH
 
 echo $PATH
 
-export LD_LIBRARY_PATH=$RNA_HOME/student_tools/flexbar-3.5.0-linux:$LD_LIBRARY_PATH
 export PICARD=$RNA_HOME/student_tools/picard.jar
 ```
 

diff --git a/_posts/0009-09-01-AWS_Setup.md b/_posts/0009-09-01-AWS_Setup.md
@@ -287,12 +287,6 @@ wget https://github.com/broadinstitute/picard/releases/download/2.26.4/picard.ja
 java -jar ~/bin/picard.jar
 ```
 
-#### Install [Flexbar](https://github.com/seqan/flexbar)
-
-```bash
-sudo apt install flexbar
-```
-
 #### Install [Regtools](https://github.com/griffithlab/regtools#regtools)
 
 ```bash

diff --git a/docker/site/0.0.2/Dockerfile b/docker/site/0.0.2/Dockerfile
@@ -11,18 +11,17 @@ LABEL "Description"="ruby environment for development of rnabio.org site"
 ################################################################################
 ##################### Install Necessary gems ############################
 
-WORKDIR /tmp
-RUN git clone https://github.com/griffithlab/rnabio.org.git
-#RUN wget https://raw.githubusercontent.com/griffithlab/rnabio.org/master/Gemfile
-#RUN wget https://raw.githubusercontent.com/griffithlab/rnabio.org/master/Gemfile.lock
 WORKDIR /tmp/rnabio.org
-RUN gem install bundler &&\
-    bundle install &&\
-    rm -rf /tmp/rnabio.org
+RUN wget https://raw.githubusercontent.com/griffithlab/rnabio.org/master/Gemfile &&\
+    wget https://raw.githubusercontent.com/griffithlab/rnabio.org/master/Gemfile.lock &&\
+    wget https://raw.githubusercontent.com/griffithlab/rnabio.org/master/alembic-jekyll-theme.gemspec &&\
+    gem install bundler &&\
+    bundle install
 WORKDIR /usr/local/bin
 RUN echo "#!/bin/bash\nbundle exec jekyll serve --host 0.0.0.0 --watch" > start_jekyll.sh &&\
     chmod +x start_jekyll.sh &&\
-    mkdir -p /opt/git/rnabio.org
+    mkdir -p /opt/git/rnabio.org &&\
+    rm -rf /tmp/rnabio.org
 WORKDIR /opt/git/rnabio.org
 
 ################################################################################