From e68600d00fbf1270e1f6e06860872e9d9d0ffa00 Mon Sep 17 00:00:00 2001
From: pdimens <pdimens@live.com>
Date: Tue, 7 May 2024 15:50:13 -0400
Subject: [PATCH] remove this folder, it's not needed anymore

---
 src/harpy/envs/__init__.py       |  0
 src/harpy/envs/align.yaml        | 15 ---------------
 src/harpy/envs/harpy.yaml        | 14 --------------
 src/harpy/envs/phase.yaml        | 11 -----------
 src/harpy/envs/qc.yaml           | 10 ----------
 src/harpy/envs/r-env.yaml        | 15 ---------------
 src/harpy/envs/variants.snp.yaml | 10 ----------
 src/harpy/envs/variants.sv.yaml  | 14 --------------
 8 files changed, 89 deletions(-)
 delete mode 100644 src/harpy/envs/__init__.py
 delete mode 100644 src/harpy/envs/align.yaml
 delete mode 100644 src/harpy/envs/harpy.yaml
 delete mode 100644 src/harpy/envs/phase.yaml
 delete mode 100644 src/harpy/envs/qc.yaml
 delete mode 100644 src/harpy/envs/r-env.yaml
 delete mode 100644 src/harpy/envs/variants.snp.yaml
 delete mode 100644 src/harpy/envs/variants.sv.yaml

diff --git a/src/harpy/envs/__init__.py b/src/harpy/envs/__init__.py
deleted file mode 100644
index e69de29bb..000000000
diff --git a/src/harpy/envs/align.yaml b/src/harpy/envs/align.yaml
deleted file mode 100644
index 19adfdb8a..000000000
--- a/src/harpy/envs/align.yaml
+++ /dev/null
@@ -1,15 +0,0 @@
-name: align
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - bwa 
-  - ema
-  - icu
-  - libzlib
-  - llvm-openmp 
-  - pysam
-  - samtools=1.19
-  - seqtk 
-  - xz
\ No newline at end of file
diff --git a/src/harpy/envs/harpy.yaml b/src/harpy/envs/harpy.yaml
deleted file mode 100644
index 605d87dfd..000000000
--- a/src/harpy/envs/harpy.yaml
+++ /dev/null
@@ -1,14 +0,0 @@
-name: harpy
-channels:
-  - conda-forge
-  - bioconda
-dependencies:
-  - bcftools =1.19
-  - mamba
-  - pandas
-  - python
-  - rich-click
-  - snakemake-minimal >7
-  - samtools
-  - seqtk
-  - tabix
\ No newline at end of file
diff --git a/src/harpy/envs/phase.yaml b/src/harpy/envs/phase.yaml
deleted file mode 100644
index 0b3de50d1..000000000
--- a/src/harpy/envs/phase.yaml
+++ /dev/null
@@ -1,11 +0,0 @@
-name: phase
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - bcftools=1.19
-  - hapcut2 
-  - pysam 
-  - samtools
-  - tabix
\ No newline at end of file
diff --git a/src/harpy/envs/qc.yaml b/src/harpy/envs/qc.yaml
deleted file mode 100644
index da64ffb43..000000000
--- a/src/harpy/envs/qc.yaml
+++ /dev/null
@@ -1,10 +0,0 @@
-name: qc
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - falco 
-  - fastp 
-  - multiqc 
-  - pysam
\ No newline at end of file
diff --git a/src/harpy/envs/r-env.yaml b/src/harpy/envs/r-env.yaml
deleted file mode 100644
index 0f71cbf90..000000000
--- a/src/harpy/envs/r-env.yaml
+++ /dev/null
@@ -1,15 +0,0 @@
-name: r_env
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - bioconductor-complexheatmap 
-  - r-circlize 
-  - r-dt 
-  - r-flexdashboard 
-  - r-ggplot2 
-  - r-ggridges 
-  - r-plotly
-  - r-stitch 
-  - r-tidyr 
\ No newline at end of file
diff --git a/src/harpy/envs/variants.snp.yaml b/src/harpy/envs/variants.snp.yaml
deleted file mode 100644
index eee04ae67..000000000
--- a/src/harpy/envs/variants.snp.yaml
+++ /dev/null
@@ -1,10 +0,0 @@
-name: snp
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - bcftools=1.19 
-  - freebayes 
-  - pysam 
-  - samtools
\ No newline at end of file
diff --git a/src/harpy/envs/variants.sv.yaml b/src/harpy/envs/variants.sv.yaml
deleted file mode 100644
index cd5a21bda..000000000
--- a/src/harpy/envs/variants.sv.yaml
+++ /dev/null
@@ -1,14 +0,0 @@
-name: sv
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - bcftools=1.19
-  - leviathan 
-  - naibr-plus 
-  - pysam 
-  - samtools 
-  - tabix 
-  - whatshap 
-  - xz
\ No newline at end of file