# HG changeset patch
# User galaxy-australia
# Date 1649052557 0
# Node ID 5c48d182d4fd1e6b57daad92cfa7e5be5cb926c6
# Parent  939be8401810c6f48b6a8f850e726fb92c788019
Deleted selected files

diff -r 939be8401810 -r 5c48d182d4fd README.rst
--- a/README.rst	Mon Apr 04 05:53:14 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
-Cactus
-======
-
-This suite contains a wrapper for the
-`Cactus <github.com/comparativeGenomicsToolkit/cactus>`__ whole-genome
-aligner and another wrapper for exporting the data it generates.
-
-Requirements
-------------
-
-The developers provide an official Docker container. However, the Docker
-container won’t run unless ``/etc/passwd`` is mounted (`see this
-issue <https://github.com/ComparativeGenomicsToolkit/cactus/issues/677>`__).
-Because of this, it is recommended to run Cactus using Singularity.
-
-Cactus uses a lot of RAM. We have tested it on Galaxy using 24 GB of RAM
-for a progressive alignment of three chromosome-level, 150 megabase
-genomes.
diff -r 939be8401810 -r 5c48d182d4fd help.md
--- a/help.md	Mon Apr 04 05:53:14 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,58 +0,0 @@
-
-**What it does**
-
-[Cactus](https://github.com/ComparativeGenomicsToolkit/cactus) is a reference-free whole-genome multiple alignment program.
-It can be used to progressively align a large number of genomes.
-
-**Usage**
-
-***Between-species mode***
-
-If you are aligning genomes from **multiple species**, you need to provide a guide tree in Newick format. Cactus uses the guide tree to progressively align genomes, meaning that it doesn't need to align all possible pairs of genomes.
-
-A Newick-formatted tree for human, chimp and gorilla genomes looks like this:
-
-```
-(((human:0.006,chimp:0.006667):0.0022,gorilla:0.008825):0.0096,orang:0.01831);
-```
-
-The numbers are the branch lengths.
-
-
-***Beta: Within-species mode***
-
-You can also run Cactus in [pangenome mode](https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md) to align genomes of multiple individuals from the **same species**. 
-In this mode you will not be able to provide a guide tree. 
-Cactus will use [minigraph](https://github.com/lh3/minigraph) to generate a graph of the input genomes and then use the graph to order the alignments.
-To use pangenome mode, select 'Within-species' in the 'Alignment mode' dropdown.
-
-**Input**
-
-The developers recommend soft-masking your genomes with RepeatMasker before running Cactus.
-RepeatMasker is available on Galaxy.
-
-If you're using Between-species mode, you need to provide labels for the fasta files that match the leaves on the guide tree.
-In the example above, you would use the label 'human' for the human fasta file.
-
-**Output**
-
-The main output of Cactus is in [HAL format](https://github.com/ComparativeGenomicsToolkit/cactus#using-the-output).
-You can use the [Cactus: export](root?tool_id=cactus_export) tool to convert the Cactus output to a VG or Multiple Alignment Format (MAF) file.
-
-
----
-
-**What it does**
-
-Converts the HAL output from [Cactus whole-genome multiple sequence aligner](root?tool_id=cactus_cactus) into other formats.
-
-**Input**
-
-A [HAL file](https://github.com/ComparativeGenomicsToolkit/cactus#using-the-output) from [Cactus](root?tool_id=cactus_cactus).
-
-**Output**
-
-Currently, you can export a pangenome in VG format, for use with [vg](https://github.com/vgteam/vg), and/or Multiple Alignment Format (MAF).
-Note that MAF is **reference-based**, so it will contain alignments to a single reference from your list of inputs (i.e. not a graph).
-By default, the first input genome will be used as the reference.
-You can override this with the 'reference genome' option.