From c4ba3bb25c55a54e383d10f38e3aa20e66da22ae Mon Sep 17 00:00:00 2001
From: Emily Zhang <64569438+emilyyzhangg@users.noreply.github.com>
Date: Tue, 1 Oct 2024 16:19:09 -0700
Subject: [PATCH] minor bug fixes before goldrush release (#142)

* minor bug fixes before goldrush release

* removing .DS_Store file

* removing mamba version pin from yml file

* repinning stable version of mamba in yml file

* Install conda for macos CI test

* Updating install conda script in yml file since last one was buggy

* Updating install conda script again
---
 README.md                   |   2 +-
 azure-pipelines.yml         |  14 +++++++++++---
 bin/goldrush                |   2 +-
 subprojects/.DS_Store       | Bin 6148 -> 0 bytes
 tests/goldrush_test_demo.sh |   2 +-
 5 files changed, 14 insertions(+), 6 deletions(-)
 delete mode 100644 subprojects/.DS_Store

diff --git a/README.md b/README.md
index 964622a..6ecec1a 100755
--- a/README.md
+++ b/README.md
@@ -15,7 +15,7 @@ GoldRush iterates through the input long reads to produce a "golden path" of rea
 2. **[GoldPolish](https://github.com/bcgsc/goldpolish)** (aka GoldRush-Edit): polishing the genome
 3. **[Tigmint-long](https://github.com/bcgsc/tigmint)**: correcting the genome
 4. **[GoldChain](https://github.com/bcgsc/ntlink)** (aka GoldRush-Link): scaffolding the genome
-5. **[GoldPolish-Target](https://github.com/bcgsc/goldpolish)**: targeted polishing the genome
+5. **[GoldPolish-Target](https://github.com/bcgsc/goldpolish)**: targeted polishing of the genome
 
 
 ## Credits
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index 3b2dadc..209d0d5 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -14,7 +14,7 @@ jobs:
     displayName: Create Anaconda environment
   - script: |
       source activate goldrush_CI
-      conda install --yes -c conda-forge mamba python=3.10 
+      conda install --yes -c conda-forge mamba=1.5.10 python=3.10 
       mamba install --yes -c conda-forge -c bioconda compilers meson gperftools sdsl-lite boost-cpp sparsehash btllib libdivsufsort minimap2 tigmint ntlink miller snakemake intervaltree  
     displayName: Install dependencies
   - script: |
@@ -41,8 +41,16 @@ jobs:
   - checkout: self
     persistCredentials: true
     submodules: true
-  - script: echo "##vso[task.prependpath]$CONDA/bin"
-    displayName: Add conda to PATH
+  - script: |
+      mkdir -p ~/miniforge3
+      curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh  -o ~/miniforge3/miniforge.sh
+      bash ~/miniforge3/miniforge.sh -b -u -p ~/miniforge3
+      rm -rf  ~/miniforge3/miniforge.sh
+      ~/miniforge3/bin/conda init bash
+      ~/miniforge3/bin/conda init zsh
+      export CONDA=$(realpath ~/miniforge3/bin)
+      echo "##vso[task.prependpath]$CONDA"
+    displayName: Install conda
   - script: conda create --yes --quiet --name goldrush_CI
     displayName: Create Anaconda environment
   - script: |
diff --git a/bin/goldrush b/bin/goldrush
index 895b2c6..fa555ea 100755
--- a/bin/goldrush
+++ b/bin/goldrush
@@ -150,7 +150,7 @@ help:
 	@echo "	goldrush-path			run GoldRush-Path"
 	@echo "	path-polish			run GoldRush-Path, then $(polisher_logs)"
 	@echo "	path-tigmint			run GoldRush-Path, then $(polisher_logs), then Tigmint-long"
-	@echo "	path-tigmint-ntLin		run GoldRush-Path, then $(polisher_logs), then Tigmint-long, then ntLink (default 5 rounds)"
+	@echo "	path-tigmint-ntLink		run GoldRush-Path, then $(polisher_logs), then Tigmint-long, then ntLink (default 5 rounds)"
 	@echo "	path-tigmint-ntLink-target	run GoldRush-Path, then $(polisher_logs), then Tigmint-long, then ntLink (default 5 rounds), then GoldPolish-Target"
 	@echo ""
 	@echo "	General options (required):"
diff --git a/subprojects/.DS_Store b/subprojects/.DS_Store
deleted file mode 100644
index 6abb19ac688d35825f1c71278825d71002ffba5c..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 6148
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zE=B_!HDYFx**D#t*KXf7yBz=!&9PqtC;@<lPM9fRv%qMae9khaCyOZ5Jq92lgaBgb
z&t-GRUsQnBZUcI1-F*16erKV)_d@C6IDH()=)3RAFj~U#l6YV^uihXG;!(BwCNkOF
z+Irr~TSe>E?aRa+bw=a3*%@Bb)rFLyH;X&oWzbF9rL7YgjXFWp9V$ZLcQNJWDu{fU
zH03z*W5sp#fK{*x?NWI%sa5M0yKy+J*pphVzK?O^U^*>W+dF$l=k15^F_O<}_8{<k
zRkmqx1}_*a)Z@t=Mxl&)I6mXfIE<_SE5Hh@ngV7Yvx=)Wah@+LzzY1h0<=Ha=!A~J
zRHNEDuu&xdVh+2NVNAb^#IX%J22+hVf+jQ-QB#E}F@&aLzisjygQ-SM2Vsg2VV*2Z
zg(B3`@&2|-2jOVsmK9(HzAHerA6kjd|I_95ze?hU6<`Jarvf6^a$8M&H*>bmy(OKs
uHu@bp8RexKKPecfqZo7PC@!Nb!+x6rM8{yN5qr@1M?lHI4J+`g3VZ+%zgx}#

diff --git a/tests/goldrush_test_demo.sh b/tests/goldrush_test_demo.sh
index 2b46499..8977d20 100755
--- a/tests/goldrush_test_demo.sh
+++ b/tests/goldrush_test_demo.sh
@@ -9,7 +9,7 @@ curl -L --output test_reads.fq https://www.bcgsc.ca/downloads/btl/goldrush/test/
 echo "Launching GoldRush"
 goldrush run reads=test_reads G=1e6 t=4 p=goldrush_test  -B
 
-l50=$(abyss-fac goldrush_test_golden_path.goldpolish-polished.span2.dist500.tigmint.fa.k40.w250.ntLink-5rounds.fa |awk '{print $3}' |tail -n1)
+l50=$(abyss-fac goldrush_test_golden_path.goldpolish-polished.span2.dist500.tigmint.fa.k40.w250.ntLink-5rounds.polished.fa |awk '{print $3}' |tail -n1)
 
 if [ -e goldrush_test_golden_path.goldpolish-polished.span2.dist500.tigmint.fa.k40.w250.ntLink-5rounds.polished.fa ] && [ ${l50} -eq 1 ]; then
   echo -e "\nTest successful!"