Merge pull request #226 from broadinstitute/dev

Dev
broadinstitute · Jun 4, 2024 · 4ed0148 · 4ed0148
2 parents 5725fc7 + 8a43013
commit 4ed0148
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Showing 11 changed files with 218 additions and 229 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -21,6 +21,7 @@ jobs:
     # The executor is the environment in which the steps below will be executed
     docker:
       - image: condaforge/mambaforge
+    resource_class: large  # 8GB of memory
     # CircleCI will report the results back to your VCS provider.
     steps:
       - checkout

diff --git a/docs/usage/getting_started.rst b/docs/usage/getting_started.rst
@@ -15,6 +15,7 @@ Installation
 	- Make sure you're not using strict channel priorities: ``conda config --set channel_priority flexible``. Otherwise, you may encounter package conflicts later when installing abc. 
 	- To install mamba: ``conda create -n mamba -c conda-forge mamba -y``
 		- We recommend mamba as using conda can take 1hr+ for setup
+		- See troubleshooting page if you run into issues
 
 
 Setup Conda Environment
@@ -123,7 +124,7 @@ biosamples config is a tsv separated file with the following columns
 	- If you dumped hic into a directory via JuicerTools, use ``juicebox``
 	- If you have a bedpe file for contact, it should be a tab delimited file containing 8 columns (chr1,start1,end1,chr2,start2,end2,name,score)
 #. HiC_resolution (int)
-	- Recommended to use 5KB (kilobases)
+	- Currently only 5KB (kilobases) is supported
 	- 5KB means dna regions are bucketed into 5KB bins and we measure contact between those bins
 #. alt_TSS (optional; not recommended to fill)
 	- Alternative TSS reference file 

diff --git a/tests/config/test_biosamples.tsv b/tests/config/test_biosamples.tsv
@@ -1,3 +1,3 @@
 biosample	DHS	ATAC	H3K27ac	default_accessibility_feature	HiC_file	HiC_type	HiC_resolution	alt_TSS	alt_genes
-K562_chr22	example_chr/chr22/ENCFF860XAE.chr22.sorted.se.bam		example_chr/chr22/ENCFF790GFL.chr22.sorted.se.bam	DHS	https://www.encodeproject.org/files/ENCFF621AIY/@@download/ENCFF621AIY.hic	hic	5000	example_chr/chr22/RefSeqCurated.170308.bed.CollapsedGeneBounds.chr22.hg38.TSS500bp.bed	example_chr/chr22/RefSeqCurated.170308.bed.CollapsedGeneBounds.chr22.hg38.bed
+K562_chr22	example_chr/chr22/ENCFF860XAE.chr22.sorted.se.bam		example_chr/chr22/ENCFF790GFL.chr22.sorted.se.bam	DHS	https://encode-public.s3.amazonaws.com/2022/05/15/0571c671-3645-4f92-beae-51dfd3f42c36/ENCFF621AIY.hic	hic	5000	example_chr/chr22/RefSeqCurated.170308.bed.CollapsedGeneBounds.chr22.hg38.TSS500bp.bed	example_chr/chr22/RefSeqCurated.170308.bed.CollapsedGeneBounds.chr22.hg38.bed
 K562_chr22_tagAlign		example_chr/chr22/chr22.sorted.tagAlign.gz		ATAC				example_chr/chr22/RefSeqCurated.170308.bed.CollapsedGeneBounds.chr22.hg38.TSS500bp.bed	example_chr/chr22/RefSeqCurated.170308.bed.CollapsedGeneBounds.chr22.hg38.bed
diff --git a/tests/test_predictor.py b/tests/test_predictor.py
@@ -7,7 +7,7 @@
 from predictor import add_hic_from_hic_file
 import pandas as pd
 
-HIC_FILE = "https://www.encodeproject.org/files/ENCFF621AIY/@@download/ENCFF621AIY.hic"
+HIC_FILE = "https://encode-public.s3.amazonaws.com/2022/05/15/0571c671-3645-4f92-beae-51dfd3f42c36/ENCFF621AIY.hic"
 
 # this file has 3k rows of E-G pairs with valid contact values
 # contact values were generated from the original doubly stochastic method

diff --git a/workflow/envs/abcenv.yml b/workflow/envs/abcenv.yml
@@ -13,6 +13,7 @@ dependencies:
   - numpy
   - pandas
   - pybigwig
+  - pulp<2.8 # Pin pulp <2.8 for snakemake: https://github.com/snakemake/snakemake/issues/2607
   - pip
   - pyarrow
   - pyranges
@@ -35,4 +36,4 @@ dependencies:
   - zlib
   - pip:
     - sphinx_rtd_theme
-    - hic-straw
+    - hic-straw