From 749ad4a544ef8616e2a36688fecf138ff868aea9 Mon Sep 17 00:00:00 2001
From: Florian Zwagemaker <f.zwagemaker@gmail.com>
Date: Thu, 4 Apr 2024 12:16:35 +0200
Subject: [PATCH] deps: explicitly state the nodefaults channel in all
 environments

deps: solve minor installation hassles for the main environment
---
 SARS2seq/workflow/envs/Alignment.yaml | 1 +
 SARS2seq/workflow/envs/Clean.yaml     | 1 +
 SARS2seq/workflow/envs/Consensus.yaml | 6 ++++--
 SARS2seq/workflow/envs/Mutations.yaml | 1 +
 SARS2seq/workflow/envs/Typing.yaml    | 1 +
 env.yml                               | 7 ++++---
 6 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/SARS2seq/workflow/envs/Alignment.yaml b/SARS2seq/workflow/envs/Alignment.yaml
index f98be81..42d1cda 100644
--- a/SARS2seq/workflow/envs/Alignment.yaml
+++ b/SARS2seq/workflow/envs/Alignment.yaml
@@ -3,6 +3,7 @@ channels:
   - bioconda
   - conda-forge
   - intel
+  - nodefaults
 dependencies:
   - python=3.7
   - minimap2==2.24
diff --git a/SARS2seq/workflow/envs/Clean.yaml b/SARS2seq/workflow/envs/Clean.yaml
index 2b14e9f..2a4ef0b 100644
--- a/SARS2seq/workflow/envs/Clean.yaml
+++ b/SARS2seq/workflow/envs/Clean.yaml
@@ -3,6 +3,7 @@ channels:
   - bioconda
   - conda-forge
   - intel
+  - nodefaults
 dependencies:
   - python=3.8
   - ampligone==1.2.1
diff --git a/SARS2seq/workflow/envs/Consensus.yaml b/SARS2seq/workflow/envs/Consensus.yaml
index 2926b26..4e18609 100644
--- a/SARS2seq/workflow/envs/Consensus.yaml
+++ b/SARS2seq/workflow/envs/Consensus.yaml
@@ -3,6 +3,7 @@ channels:
   - bioconda
   - conda-forge
   - intel
+  - nodefaults
 dependencies:
   - python=3.7
   - libffi==3.3
@@ -14,5 +15,6 @@ dependencies:
   - tqdm=4.62
   - pip
   - pip:
-    - gffpandas>=1.2
-    - git+https://github.com/RIVM-bioinformatics/TrueConsense.git@v0.5.0
+      #this is temporary until gffpandas has a patched version released on conda/pypi or when we port the required function in TrueConsense to AminoExtract
+    - git+https://github.com/florianzwagemaker/gffpandas.git@main
+    - git+https://github.com/RIVM-bioinformatics/TrueConsense.git@v0.5.1
diff --git a/SARS2seq/workflow/envs/Mutations.yaml b/SARS2seq/workflow/envs/Mutations.yaml
index 6cf8fd4..c1917de 100644
--- a/SARS2seq/workflow/envs/Mutations.yaml
+++ b/SARS2seq/workflow/envs/Mutations.yaml
@@ -3,5 +3,6 @@ channels:
   - bioconda
   - conda-forge
   - intel
+  - nodefaults
 dependencies:
   - bcftools==1.14
\ No newline at end of file
diff --git a/SARS2seq/workflow/envs/Typing.yaml b/SARS2seq/workflow/envs/Typing.yaml
index 04d84c4..2c84a69 100644
--- a/SARS2seq/workflow/envs/Typing.yaml
+++ b/SARS2seq/workflow/envs/Typing.yaml
@@ -3,6 +3,7 @@ channels:
   - bioconda
   - conda-forge
   - intel
+  - nodefaults
 dependencies:
   - python=3.7
   - libffi==3.3
diff --git a/env.yml b/env.yml
index 0cd0ac5..b770c5c 100644
--- a/env.yml
+++ b/env.yml
@@ -3,10 +3,11 @@ channels:
   - bioconda
   - conda-forge
   - intel
+  - nodefaults
 dependencies:
-  - python=3.7
-  - conda=4.11
-  - mamba
+  - python=3.8
+  # - conda=4.11
+  - mamba>1.0
   - drmaa==0.7.9
   - snakemake==7.12.1
   - tabulate==0.8.10