Merge pull request #598 from ComparativeGenomicsToolkit/graphmap-split4

Prep release 2.0.4

README.md

@@ -42,10 +42,10 @@ There are many different ways to install and run Cactus:
 
 #### Docker Image
 
-Cactus docker images are hosted on [quay](https://quay.io/repository/comparative-genomics-toolkit/cactus).  The image for the latest release is listed on the [Releases Page](https://github.com/ComparativeGenomicsToolkit/cactus/releases).  Here is an command line to run the included evolver mammals example with release 2.0.3
+Cactus docker images are hosted on [quay](https://quay.io/repository/comparative-genomics-toolkit/cactus).  The image for the latest release is listed on the [Releases Page](https://github.com/ComparativeGenomicsToolkit/cactus/releases).  Here is an command line to run the included evolver mammals example with release 2.0.4
 ```
 wget https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/master/examples/evolverMammals.txt
-docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.0.3 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal --root mr --binariesMode local
+docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.0.4 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal --root mr --binariesMode local
 
 ```
 

ReleaseNotes.md

@@ -1,12 +1,11 @@
-# Release 2.1.0
+# Release 2.0.4   2021-11-12
 
-This release features improvements to the pangenome pipeline.
+This release fixes a bug introduced in 2.0.0 where ancestral sequences could not be specified in the input, which prevented the recommended producedure for updating existing alignments from working. 
 
-- Turn recoverable chains length down to 10kb to prevent CAF from pulling apart more than BAR can realign in a single POA window
-- Automatically strip minigraph contigs out of input to `cactus-align`.  This leads to bigger blocks and smoother graphs (but requires above change)
-- Fix up clipping option in the preprocessor to work with `--fileMask` option, as well as to produce fasta contig names that `hal2vg` accepts (and the browser allows).  Clipping is now to be preferred over the various `--maskFilter and --barMaskFilter` options used to ignore softmasked sequence.
+- Fix `Assertion `cap_getSequence(cap) == sequence' failed` error when ancestral fasta provided in input seqfile.
+- Several minor pangenome updates, mostly in `cactus-graphmap-join`
 
-# Release 2.0.3
+# Release 2.0.3   2021-07-22
 
 This release fixes some issues in pangenome normalization and CAF running time.
 

build-tools/downloadPangenomeTools

@@ -256,9 +256,7 @@ fi
 
 # vg
 cd ${pangenomeBuildDir}
-#tempoarary hack until 1.35.0 is actually released
-wget -q http://public.gi.ucsc.edu/~hickey/vg
-#wget -q https://github.com/vgteam/vg/releases/download/v1.35.0/vg
+wget -q https://github.com/vgteam/vg/releases/download/v1.36.0/vg
 chmod +x vg
 if [[ $STATIC_CHECK -ne 1 || $(ldd vg | grep so | wc -l) -eq 0 ]]
 then

src/cactus/shared/common.py

@@ -383,7 +383,7 @@ def getDockerImage():
 
 def getDockerRelease(gpu=False):
     """Get the most recent docker release."""
-    r = "quay.io/comparative-genomics-toolkit/cactus:v2.0.3"
+    r = "quay.io/comparative-genomics-toolkit/cactus:v2.0.4"
     if gpu:
         r += "-gpu"
     return r