From 21600c9fa06ed64e369647eb4fb3570c156a499c Mon Sep 17 00:00:00 2001
From: Aaron <aaronleefeller@gmail.com>
Date: Tue, 26 Mar 2024 14:24:44 -0500
Subject: [PATCH 1/5] Update README.md

---
 README.md | 34 ++++++----------------------------
 1 file changed, 6 insertions(+), 28 deletions(-)

diff --git a/README.md b/README.md
index 26446bf..817ebc3 100644
--- a/README.md
+++ b/README.md
@@ -6,7 +6,7 @@
 ## Installation
 There are two methods for installation; one uses pip and should be more user friendly.
 
-## Installation from PyPI (recommended)
+## Installation from PyPI
 
 The following includes steps to install dependencies.
 
@@ -17,28 +17,11 @@ $ conda activate <your-env-name>
 ```
 ### Install other dependencies:
 ```bash
-$ conda install mamba -c conda-forge
+$ conda activate <environment_name>
 $ pip install cinful
-$ cinful_init
+$ conda install seqkit=0.15.0 mafft=7.475 hmmer=3.3.1 blast=2.9.0 diamond=2.0.11 pandas=1.2.4 numpy=1.24.4 biopython=1.76 snakemake=6.3.0 prodigal=2.6.3 pyhmmer=0.3.0
+$ pip install pyTMHMM==1.3.2 seqhash==1.0.0 blake3==0.2.0
 ```
-#### Dependencies installed with $ cinful_init
-* seqkit=0.15.0
-* mafft=7.475
-* hmmer=3.3.1
-* blast=2.9.0
-* diamond=2.0.11
-* pandas=1.2.4
-* numpy=1.19.2
-* biopython=1.76
-* snakemake=6.3.0
-* prodigal=2.6.3
-* pyhmmer=0.3.0
-
-##### PyPI dependencies:
-* pyTMHMM==1.3.2
-* seqhash==1.0.0
-* blake3==0.2.0
-
 
 If installed properly, running `cinful -h` will produce the following output:
 
@@ -62,9 +45,8 @@ optional arguments:
 
 ## Installation test
 
-I am working on a test to verify installation. As a workaround, you are able to download a test genome that contains microcin, MFP, PCAT, and immunity protein from https://github.com/wilkelab/cinful/blob/main/test/.
-
-Once you've downloaded the test file, you can run *cinful* on the contents and compare the output to the results stored in the directory cinful_out.
+Run cinful on the cinful/test directory as such
+$ cinful -d path/to/cinful/test -o <name_your_test>
 
 ## Usage notes
 
@@ -105,10 +87,6 @@ git clone https://github.com/wilkelab/cinful.git
 ```
 All software dependencies needed to run *cinful* are available through conda and are specified in `cinful_conda.yml`, the following helper script can be used to generate the *cinful* conda environment `scripts/build_conda_env.sh`, to run this script, you will need to have conda installed, as well as mamba (which helps speed up installation). To install mamba, use the following command:
 
-```bash
-conda install mamba -c conda-forge
-```
-
 To build the environment, run:
 ```bash
 bash env/build_conda_env.sh

From df21811181cc178462b26114da1cf671d24802ad Mon Sep 17 00:00:00 2001
From: Aaron <aaronleefeller@gmail.com>
Date: Tue, 26 Mar 2024 14:25:55 -0500
Subject: [PATCH 2/5] Update build_conda_env.sh

---
 cinful/env/build_conda_env.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cinful/env/build_conda_env.sh b/cinful/env/build_conda_env.sh
index e1f2bf9..9699b8c 100644
--- a/cinful/env/build_conda_env.sh
+++ b/cinful/env/build_conda_env.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-mamba create -n cinful
-mamba env update -n cinful --file cinful_conda.yml
+conda create --name cinful python=3.8.13 pip
+conda env update -n cinful --file cinful_conda.yml

From 170513e82bfb6cb5cc2d4fc5fbe06a70a2a561aa Mon Sep 17 00:00:00 2001
From: Aaron <aaronleefeller@gmail.com>
Date: Tue, 26 Mar 2024 14:26:48 -0500
Subject: [PATCH 3/5] Update cinful_conda.yml

---
 cinful/env/cinful_conda.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cinful/env/cinful_conda.yml b/cinful/env/cinful_conda.yml
index 02e2cbc..3376c04 100644
--- a/cinful/env/cinful_conda.yml
+++ b/cinful/env/cinful_conda.yml
@@ -5,18 +5,18 @@ channels:
   - bioconda
 dependencies:
   - python=3.8.13
+  - pip
   - seqkit=0.15.0
   - mafft=7.475
   - hmmer=3.3.1
   - blast=2.9.0
   - diamond=2.0.11
   - pandas=1.2.4
-  - numpy=1.19.2
+  - numpy=1.24.4
   - biopython=1.76
   - snakemake=6.3.0
   - prodigal=2.6.3
   - pyhmmer=0.3.0
-  - pip
   - pip:
     - pyTMHMM==1.3.2
     - seqhash==1.0.0

From 751826567d4a11406a43c3b24b5d0bb2fdd7b5bf Mon Sep 17 00:00:00 2001
From: Aaron <aaronleefeller@gmail.com>
Date: Tue, 26 Mar 2024 14:31:46 -0500
Subject: [PATCH 4/5] Update README.md

---
 README.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 817ebc3..2ee29af 100644
--- a/README.md
+++ b/README.md
@@ -89,7 +89,8 @@ All software dependencies needed to run *cinful* are available through conda and
 
 To build the environment, run:
 ```bash
-bash env/build_conda_env.sh
+$ conda create --name cinful python=3.8.13 pip
+$ conda env update -n cinful --file path/to/cinful/env/cinful_conda.yml
 ```
 
 Once setup is complete, you can activate the environment with:

From eced7efb52f1e4ec891da914b096716770588393 Mon Sep 17 00:00:00 2001
From: Aaron <aaronleefeller@gmail.com>
Date: Tue, 26 Mar 2024 14:33:03 -0500
Subject: [PATCH 5/5] Update README.md

---
 README.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/README.md b/README.md
index 2ee29af..280a1a9 100644
--- a/README.md
+++ b/README.md
@@ -46,7 +46,9 @@ optional arguments:
 ## Installation test
 
 Run cinful on the cinful/test directory as such
+```bash
 $ cinful -d path/to/cinful/test -o <name_your_test>
+```
 
 ## Usage notes