From 39c1cc477f1fcfd04b4c8d0a51c18083fdd12e8b Mon Sep 17 00:00:00 2001
From: Silas Kieser <silas.kieser@gmail.com>
Date: Wed, 26 Jun 2024 10:14:21 +0200
Subject: [PATCH 1/2] more mem for gtdb align

---
 workflow/rules/gtdbtk.smk | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/workflow/rules/gtdbtk.smk b/workflow/rules/gtdbtk.smk
index 02d630b0..456504b7 100644
--- a/workflow/rules/gtdbtk.smk
+++ b/workflow/rules/gtdbtk.smk
@@ -32,6 +32,8 @@ checkpoint align:
     output:
         directory(f"{gtdb_dir}/align"),
     threads: config["threads"]
+    resources:
+        mem_mb=config["large_mem"] * 1000,
     conda:
         "../envs/gtdbtk.yaml"
     log:

From b34c3589aaea8268304faff628e637bda99f2571 Mon Sep 17 00:00:00 2001
From: Silas Kieser <silas.kieser@gmail.com>
Date: Wed, 26 Jun 2024 10:14:42 +0200
Subject: [PATCH 2/2] my dram

---
 workflow/envs/dram.yaml | 23 +++++++++++++++++++++--
 1 file changed, 21 insertions(+), 2 deletions(-)

diff --git a/workflow/envs/dram.yaml b/workflow/envs/dram.yaml
index 820601af..6025b0a9 100644
--- a/workflow/envs/dram.yaml
+++ b/workflow/envs/dram.yaml
@@ -2,5 +2,24 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - dram >= 1.4.6, <1.5 #Shold define all correct verrsions See https://github.com/bioconda/bioconda-recipes/pull/41518
-
+  - python >=3.8
+  - altair >=4
+  - networkx
+  - numpy
+  - openpyxl
+  - pandas >=1.5, <2
+  - scikit-bio >=0.5.8, <0.6
+  - sqlalchemy
+  - prodigal
+  - scipy >=1.9
+  - mmseqs2 >10.6d92c
+  - hmmer
+  - trnascan-se >=2
+  - barrnap
+  - ruby
+  - parallel
+  - wget
+  - curl
+  - pip
+  - pip:
+    - git+https://github.com/SilasK/DRAM.git
\ No newline at end of file