Update to Pelican 4.7.1

Update "make html" and "make serve" targets

pelican-toc no longer works
(ingwinlu/pelican-toc#20);
using built-in Python-Markdown TOC

Dockerfile

@@ -6,6 +6,8 @@ RUN yum -y install git python3-pip httpd
 
 RUN echo -e "ServerName ${HOSTNAME}\n" >> /etc/httpd/conf/httpd.conf
 
+# https://github.com/pypa/pip/issues/10219
+ENV LC_ALL=en_US.UTF-8
 ADD requirements.txt /tmp/requirements.txt
 RUN pip3 install -r /tmp/requirements.txt
 

Makefile

@@ -1,4 +1,3 @@
-PY?=python3
 PELICAN?=pelican
 PELICANOPTS=--relative-urls -t informatics-theme
 
@@ -67,7 +66,7 @@ prod:
 
 html:
 	mkdir -p $(OUTPUTDIR)
-	$(PELICAN) $(INPUTDIR) -o $(OUTPUTDIR) -s $(CONFFILE) $(PELICANOPTS)
+	$(PELICAN) $(INPUTDIR) -o $(OUTPUTDIR) -s $(CONFFILE) $(PELICANOPTS) --delete-output-directory
 
 clean:
 	[ ! -d $(OUTPUTDIR) ] || rm -rf $(OUTPUTDIR)
@@ -77,9 +76,9 @@ regenerate:
 
 serve:
 ifdef PORT
-	cd $(OUTPUTDIR) && $(PY) -m pelican.server $(PORT)
+	$(PELICAN) --listen --autoreload --output $(OUTPUTDIR) --port $(PORT)
 else
-	cd $(OUTPUTDIR) && $(PY) -m pelican.server
+	$(PELICAN) --listen --autoreload --output $(OUTPUTDIR)
 endif
 
 serve-global:

content/adding-a-new-sequencing-price.md

@@ -5,6 +5,7 @@ Tags: Next-Gen Sequencing, Bauer Core, MiniLIMS
 Author: Michele Clamp
 Summary: How to add a new Sequencing Price to the Bauer Core MiniLIMS system
 
+[TOC]
 
 ## Create a new Sequencing Price record
 
@@ -73,4 +74,4 @@ For historical reasons some of the sequencing prices are treated differently as
 
     Submission run type    Price Display_Name
     Standard_v4            “Standard Run (v4) <1|2> x <readlen> bp"
-    Standard_v3            “Standard Run <1|2> x <readlen> bp"
+    Standard_v3            “Standard Run <1|2> x <readlen> bp"

content/basic-unix-workshop.md

@@ -5,6 +5,7 @@ Author: Michele Clamp
 Tags: Linux, Workshop
 Summary: This tutorial is intended for people completely new to unix and command line driven analysis.  It introduces how to navigate the unix filesystem, make and delete files and directories and be able to list the contents of files and directories.
 
+[TOC]
 
 ## Prerequisites
 

content/bauer-sequencing-core.md

@@ -5,6 +5,8 @@ Author: Michele Clamp
 Tags: Next-Gen Sequencing, Bauer Core
 Summary: Our core sequencing service has two Illumina HiSeqs and a MiSeq.  The FAS Informatics group is committed to providing a fast basecalling and QC service for all users of the facility.   Beyond this we strongly encourage people to [get in contact with us](mailto:informatics@fas.harvard.edu) and we’ll be happy to discuss things further.  We aim to work alongside researchers with the intention of spreading knowledge and enabling people to run analyses themselves.   As we grow we are building workflows and pipelines to enable more people to be self sufficient in bioinformatics analysis.
 
+[TOC]
+
 Our core sequencing service has two Illumina HiSeqs and a MiSeq.  The FAS Informatics group is committed to providing a fast basecalling and QC service for all users of the facility.   Beyond this we strongly encourage people to [get in contact with us](mailto:informatics@fas.harvard.edu) and we’ll be happy to discuss things further.  We aim to work alongside researchers with the intention of spreading knowledge and enabling people to run analyses themselves.   As we grow we are building workflows and pipelines to enable more people to be self sufficient in bioinformatics analysis.
 
 ## Support 

content/cactus.md

@@ -6,6 +6,8 @@ Category: Software
 Tags: Multiple Sequence Alignment, Singularity
 Summary: How to run Cactus on the FASRC Cluster
 
+[TOC]
+
 ## Introduction
 
 [Cactus](https://github.com/ComparativeGenomicsToolkit/cactus) performs Multiple Sequence Alignment on whole genomes.

content/differential-expression-with-deseq2-mouse-immune-cells.md

@@ -5,6 +5,7 @@ Author: Tim Sackton
 Tags: Differential Expression, Mouse
 Summary: This tutorial is intended for diffeq
 
+[TOC]
 
 ## Mouse immune cells
 

content/differential-expression-with-deseq2.md

@@ -5,6 +5,8 @@ Author: Tim Sackton
 Tags: Differential Expression, Drosophila melanogaster
 Summary: This tutorial is intended for diffeq
 
+[TOC]
+
 ## Drosophila melanogaster
 
 This document and the data used in this example can be found at:

content/enhancer-postdoc.md

@@ -3,6 +3,8 @@ Date: 2021-08-17
 Category: Employment
 Author: Tim Sackton
 
+[TOC]
+
 ## Postdoctoral Positions in Comparative or Statistical Genomics
 
 We are hiring two postdoctoral fellows to work on an NIH-funded project focused on the comparative and population genomics of conserved non-coding elements in birds, building on our published work on [PhyloAcc](https://doi.org/10.1093/molbev/msz049), a program to infer evolutionary forces acting on non-coding sequences in a phylogenetic context.

content/genomic-ranges-workshop.md

@@ -5,6 +5,7 @@ Author: Michele Clamp
 Tags: Genome, R, bedtools
 Summary: This tutorial provides useful tips for manipulating genomic range data.
 
+[TOC]
 
 Many kinds of genomic data can be represented as **ranges**:
 
@@ -399,4 +400,4 @@ Are human-specific neural crest enhancers more or less likely to overlap stem ce
 <div class="exercises">
 Exercise 
 <ul><li>Read in your bedtools count output and compare to the R output. Are there any differences? If so why do you think that is?</li></ul>
-</div>
+</div>

content/grep_intro.md

@@ -5,6 +5,7 @@ Author: Danielle Khost
 Tags: grep, unix
 Summary: This tutorial provides useful tips for using grep for bioinformatics
 
+[TOC]
 
 # Manipulating files with grep
 ## What is grep?

content/helium-minilims-billing-operations.md

@@ -5,6 +5,7 @@ Tags: Helium
 Author: Michele Clamp
 Summary: Billing through the Helium MiniLIMS
 
+[TOC]
 
 The Helium LIMS tracks dewars (Helium_Dewar, Helium_Dewar_Request) that have been requested and delivered.  When they are delivered they are weighed and  the reading saved Helium_Dewar_Reading).  At the end of the month these delivered dewars are charged by the volume of Helium delivered.  This is calculated by converting from weight to volume of Helium liquid. 
 

content/igv-workshop.md

@@ -5,6 +5,8 @@ Author: Michele Clamp
 Tags: IGV, Visualization
 Summary: This tutorial provides useful tips for IGV analysis.
 
+[TOC]
+
 ## Prerequisites and Installation.
 
 Note:  The IGV user guide [http://www.broadinstitute.org/software/igv/UserGuide](http://www.broadinstitute.org/software/igv/UserGuide) is extremely good and has all this information and much more.  

content/intermediate-unix-workshop.md

@@ -5,7 +5,7 @@ Author: mclamp@harvard.edu
 Tags: Linux, Workshop
 Summary: This tutorial is intended for people who are familiar with the basics of unix but want to learn more about manipulating files and running commands.
 
-
+[TOC]
 
 
 ## 1. Introduction and prerequisites

content/intro-to-r-review.md

@@ -5,6 +5,8 @@ Author: Tim Sackton
 Tags: R
 Summary: This is a review of some R basics.
 
+[TOC]
+
 This document and the data in this example can be found at:
 
 `/n/ngsdata/workshops/2015_March`

content/intro-to-r.md

@@ -5,6 +5,8 @@ Author: Tim Sackton
 Tags: R
 Summary: This is a basic introduction to the R programming language.  The tutorial is not specific to Linux or the Cannon cluster.
 
+[TOC]
+
 R is a functional programming language, which means that most of what one does is apply functions to objects.
 
 We will begin with a brief introduction to R objects and how functions work, and then focus on getting data into R, manipulating that data in R, and generating basic summary statistics.

content/jbrowse.md

@@ -6,6 +6,8 @@ Category: Software
 Tags: Genome Annotation, JBrowse, Open OnDemand
 Summary: How to launch JBrowse on the FASRC Cluster with Open OnDemand
 
+[TOC]
+
 ## Introduction
 
 [JBrowse](https://jbrowse.org/) is a web-based genome browser for visualizing genomic features in common file formats, such as variants (VCF), genes (GFF3, BigBed) and gene expression (BigWig), and sequence alignments (BAM, CRAM, and GFF3).

content/maker.md

@@ -6,6 +6,8 @@ Category: Software
 Tags: Genome Annotation, MAKER
 Summary: How to run MAKER on the FASRC Cluster
 
+[TOC]
+
 ## Introduction
 
 [MAKER](http://www.yandell-lab.org/software/maker.html)[^maker2]<sup>,</sup>[^maker] is a popular genome annotation pipeline for both prokaryotic and eukaryotic genomes.

content/minilims-pre-billing-checks.md

@@ -5,6 +5,8 @@ Tags: MiniLIMS
 Author: Michele Clamp
 Summary: Billing checks to do before invoicing.
 
+[TOC]
+
 Before invoices can be generated there are a set of billing checks that can be run that check everything is valid and can proceed to invoicing.  These things are : 
 
 * Each group has the right status (HARVARD,OUTSIDE_ACADEMIC,COMMERCIAL) 

content/picrust-on-odyssey.md

@@ -5,6 +5,8 @@ Category: Software
 Tags: PICRUSt, Python, Odyssey, Anaconda
 Summary: Setup PICRUSt on Odyssey
 
+[TOC]
+
 From the [Picrust website](http://picrust.github.io/picrust/):
 
     PICRUSt (pronounced “pie crust”) is a bioinformatics software package 

content/psmc-journal-club-walkthrough.md

@@ -5,6 +5,8 @@ Author: Tim Sackton
 Tags: Journal Club
 Summary: Walkthrough of Pairwise Sequentially Markovian Coalescent (PSMC) models
 
+[TOC]
+
 ## Introduction and setup
 
 The Pairwise Sequentially Markovian Coalescent (PSMC) model uses information in the complete diploid sequence of a single individual to infer the history of population size changes. Originally published in 2011 ([Li and Durbin 2011](http://www.nature.com/nature/journal/v475/n7357/full/nature10231.html)), it has become a very popular tool in the world of genomics. In this tutorial, we walk through the steps to generate the necessary input data for PSMC and run it on recently published [data from woolly mammoths (Palkopoulou et al., 2015)](http://www.sciencedirect.com/science/article/pii/S0960982215004200). 
@@ -131,4 +133,4 @@ Finally, we make the PSMC plot, using the per-generation mutation rate `-u` and
     :::bash
     $PSMC_HOME/utils/psmc_plot.pl -u 3.83e-08 -g 31 -p P964_plot P964.psmc
 
-Note that this script can be found at `/n/regal/informatics/workshops/PSMC_20150911/psmc.sbatch`.
+Note that this script can be found at `/n/regal/informatics/workshops/PSMC_20150911/psmc.sbatch`.

content/python-on-cannon.md

@@ -5,6 +5,8 @@ Category: Software
 Tags: Unix, Python, Cannon
 Summary: Using Python on the Cannon cluster
 
+[TOC]
+
 This page describes the use of Python on the Cannon cluster.  See also the [RC Website](https://www.rc.fas.harvard.edu/resources/documentation/software-on-the-cluster/python/)
 
 ## The Cannon system Python is 2.7.5 and you can't do much with it

content/python-on-odyssey.md

@@ -5,6 +5,8 @@ Category: Software
 Tags: Unix, Python, Odyssey
 Summary: Using Python on the Odyssey cluster
 
+[TOC]
+
 *Updated for Odyssey 3*
 
 This page describes the use of Python on the Odyssey cluster.  See also the [RC Website](https://www.rc.fas.harvard.edu/resources/documentation/software-on-odyssey/python/) and the [Practical Python on Odyssey tutorial]({filename}/practical-python-on-odyssey.md)

content/quick-intro-to-bwa.md

@@ -5,6 +5,8 @@ Author: Nathan Weeks
 Tags: grep, unix
 Summary: This tutorial provides a basic overview of using bwa to align fastqs to a reference genome
 
+[TOC]
+
 ## Aligning Reads to a Reference Genome with BWA
 ### Bioinformatics Coffee Chat - April 7, 2020
 ### Programs used in this session

content/rsem_example.md

@@ -5,6 +5,7 @@ Category: Tutorials
 Tags: Next-Gen Sequencing, Transcriptome, RNA-seq Quantitation, Differential Expression, RSEM
 Summary: An example of quantifying RNA-seq expression with RSEM on Odyssey cluster
 
+[TOC]
 
 [RSEM](http://deweylab.github.io/RSEM/README.html) is a software package for estimating gene and isoform expression levels from single-end or paired-end RNA-Seq data. The software works with transcriptome sequences and does not require a reference genome. It can either perform the read alignment step prior to quantification, or take an alignment (bam) file as input, so long as the alignment settings are appropriate for RSEM. Currently, RSEM can perform the alignment step with three different aligners: bowtie, bowtie2, or STAR. It uses the Expectation Maximization (EM) algorithm to estimate abundances at the isoform and gene levels.
 

content/unix-command-line-tips-and-tricks.md

@@ -4,6 +4,8 @@ Category: Tutorials
 Tags: Unix
 Summary: This basic unix tutorial will get you up and running for making files, listing directories and running single commands.   It will show you what you need for about 80% of your command line work.
 
+[TOC]
+
 This basic unix tutorial will get you up and running for making files, listing directories and running single commands.   It will show you what you need for about 80% of your command line work.
 
 If you find yourself at the command line a lot and have a lot of files to process then there are built in features on the bash command line (or shell) to help you.

pelicanconf.py

@@ -8,7 +8,6 @@
                 '../pelican-plugins/tipue_search/pelican/plugins/']
 PLUGINS = ['tag_cloud.tag_cloud',
            'interlinks',
-           'pelican-toc',
            'tipue_search',
            'rmd_reader',
            'pin_to_top',
@@ -33,15 +32,10 @@
             'linenums' : False,
             'guess_lang' : False,
         },
+        "markdown.extensions.toc": {"title": "Table of Contents"},
     }
 }
 
-TOC = {
-    'TOC_HEADERS' : '^h[1-3]',  # What headers should be included in the generated toc
-                                # Expected format is a regular expression
-    'TOC_RUN'     : 'true'      # Default value for toc generation, if it does not evaluate
-                                # to 'true' no toc will be generated
-}
 AUTHOR = u'Aaron Kitzmiller'
 SITENAME = u'Harvard FAS Informatics'
 SITEURL = 'https://informatics.fas.harvard.edu'

requirements.txt

@@ -1,5 +1,5 @@
 Pygments==2.11.2
 Markdown==3.3.6
 beautifulsoup4==4.10.0
-pelican==3.7.1
+pelican==4.7.1
 icalendar==4.0.9