removed mamba installation in Google Cloud

NIGMS · Feb 10, 2025 · 2a79677 · 2a79677
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diff --git a/AWS/tutorial_1-bismark.ipynb b/AWS/tutorial_1-bismark.ipynb
@@ -89,14 +89,7 @@
    "source": [
     "#### Installation of the tools for Tutorial 1 and 2 using <code>mamba</code>\n",
     "\n",
-    "[**mamba**](https://mamba.readthedocs.io/en/latest/user_guide/mamba.html) is a re-implementation of the conda package manager in C++. It uses the same commands and configuration options as conda. The only difference is that you should still use conda for activation and deactivation."
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "f0dbeb53-d416-40a3-b5b9-64ea7e58ea62",
-   "metadata": {},
-   "source": [
+    "[**mamba**](https://mamba.readthedocs.io/en/latest/user_guide/mamba.html) is a re-implementation of the conda package manager in C++. Using mamba and bioconda, install the tools that will be used in this tutorial.\n",
     "<div class= \"alert alert-block alert-info\"><b>Tip</b>: use <code>\\</code> to break a long command into multiple lines</div>"
    ]
   },

diff --git a/GoogleCloud/tutorial_1-bismark.ipynb b/GoogleCloud/tutorial_1-bismark.ipynb
@@ -101,43 +101,6 @@
     "</div>"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "8dea8fc8-2a8a-44a1-9fa6-4ae59593d887",
-   "metadata": {},
-   "source": [
-    "#### Mamba \n",
-    "\n",
-    "[**mamba**](https://mamba.readthedocs.io/en/latest/user_guide/mamba.html) is a re-implementation of the conda package manager in C++. It uses the same commands and configuration options as conda. The only difference is that you should still use conda for activation and deactivation. Once conda is installed, we will install `mamba` and use it to install all the tools we are going to use in Tutorial 1 and 2. \n",
-    "> **Installation**: conda -> mamba -> other tools\n",
-    "\n",
-    "The script below installs `mamba` via Miniforge."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "918ebef6-99e3-4096-b2d1-2f183c626f92",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "! curl -L -O https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh\n",
-    "! bash Miniforge3-$(uname)-$(uname -m).sh -b -p $HOME/miniforge"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "59a0266e-9afa-4695-af55-ece62a3713be",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#This need to be run at the start of every notebook\n",
-    "#add to your path\n",
-    "import os\n",
-    "os.environ[\"PATH\"] += os.pathsep + os.environ[\"HOME\"]+\"/miniforge/bin\""
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "37bdd323-c35b-4e41-a623-24ee7e263e11",
@@ -151,6 +114,7 @@
    "id": "f0dbeb53-d416-40a3-b5b9-64ea7e58ea62",
    "metadata": {},
    "source": [
+    "[**mamba**](https://mamba.readthedocs.io/en/latest/user_guide/mamba.html) is a re-implementation of the conda package manager in C++. Using mamba and bioconda, install the tools that will be used in this tutorial.\n",
     "<div class= \"alert alert-block alert-info\"><b>Tip</b>: use <code>\\</code> to break a long command into multiple lines</div>"
    ]
   },

diff --git a/GoogleCloud/tutorial_2-metilene.ipynb b/GoogleCloud/tutorial_2-metilene.ipynb
@@ -85,7 +85,7 @@
     "\n",
     "### Install metilene\n",
     "\n",
-    "If you've followed the previous Bismark tutorial (tutorial_1-bismark.ipynb), metilene should already be installed in the instance. If not, please use the following command to install metilene: `! conda install -y -c conda-forge -c bioconda samtools=1.15.* metilene`"
+    "If you've followed the previous Bismark tutorial (tutorial_1-bismark.ipynb), metilene should already be installed in the instance. If not, please use the following command to install metilene: `! mamba install -y -c conda-forge -c bioconda samtools=1.15.* metilene`"
    ]
   },
   {
@@ -136,7 +136,7 @@
    "outputs": [],
    "source": [
     "# Sort all the methylation files\n",
-    "!for file_name in Tutorial_2/*bedGraph.gz; do \\\n",
+    "! for file_name in Tutorial_2/*bedGraph.gz; do \\\n",
     "    sortBed -i ${file_name} > ${file_name//_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz/.bedgraph}; \\\n",
     "done;"
    ]
@@ -233,7 +233,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!metilene -a serum -b 2i Tutorial_2/metilene.input | sort -V -k1,1 -k2,2n > Tutorial_2/metilene_denovo.output"
+    "! metilene -a serum -b 2i Tutorial_2/metilene.input | sort -V -k1,1 -k2,2n > Tutorial_2/metilene_denovo.output"
    ]
   },
   {
@@ -259,7 +259,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!metilene -a serum -b 2i -f 2 -B Tutorial_1/fastq/cpgIslandExt_mm39_chr6.bed Tutorial_2/metilene.input | sort -V -k1,1 -k2,2n > Tutorial_2/metilene_cgi.output"
+    "! metilene -a serum -b 2i -f 2 -B Tutorial_1/fastq/cpgIslandExt_mm39_chr6.bed Tutorial_2/metilene.input | sort -V -k1,1 -k2,2n > Tutorial_2/metilene_cgi.output"
    ]
   },
   {
@@ -286,8 +286,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!metilene_output.pl -q Tutorial_2/metilene_denovo.output -o Tutorial_2/denovo -a serum -b 2i\n",
-    "!metilene_output.pl -q Tutorial_2/metilene_cgi.output -o Tutorial_2/cgi -a serum -b 2i"
+    "! metilene_output.pl -q Tutorial_2/metilene_denovo.output -o Tutorial_2/denovo -a serum -b 2i\n",
+    "! metilene_output.pl -q Tutorial_2/metilene_cgi.output -o Tutorial_2/cgi -a serum -b 2i"
    ]
   },
   {
@@ -411,7 +411,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!pip install jupytercards --quiet\n",
+    "! pip install jupytercards --quiet\n",
     "from jupytercards import display_flashcards\n",
     "display_flashcards('../quiz_files/f2.json')"
    ]
@@ -423,7 +423,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!pip install jupyterquiz --quiet\n",
+    "! pip install jupyterquiz --quiet\n",
     "from jupyterquiz import display_quiz\n",
     "display_quiz('../quiz_files/q2.json')"
    ]

diff --git a/GoogleCloud/tutorial_4-methylseq2.ipynb b/GoogleCloud/tutorial_4-methylseq2.ipynb
@@ -424,7 +424,7 @@
    "outputs": [],
    "source": [
     "#faster way to compress the files\n",
-    "!pigz Tutorial_4/sra_download/SRR*"
+    "! pigz Tutorial_4/sra_download/SRR*"
    ]
   },
   {
@@ -607,7 +607,7 @@
    "outputs": [],
    "source": [
     "#use the file names listed in here\n",
-    "!ls null/pipeline_info"
+    "! ls null/pipeline_info"
    ]
   },
   {

diff --git a/GoogleCloud/tutorial_5-BonusNotebook.ipynb b/GoogleCloud/tutorial_5-BonusNotebook.ipynb
@@ -64,49 +64,15 @@
    "id": "27af056b-5062-41e4-968c-d363e9420d7d",
    "metadata": {},
    "source": [
-    "## Get Started\n",
-    "The dependencies are installed the same way, so we run the next few cells the same way as in Tutorial 1. Try to install mamba below."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "f2d4f954-2881-43b9-9f32-839b5fd8a6b5",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "<YOUR COMMAND HERE>"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "d5c499de-f301-4991-85de-ec2e4b2beb41",
-   "metadata": {},
-   "source": [
-    "<details>\n",
-    "  <summary>Click for help</summary>\n",
-    "    \n",
-    "  Make sure you include the `!` in front of your command if it is a bash command.\n",
-    "    \n",
-    "   \n",
-    "`! curl -L -O https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh`\n",
-    "`! bash Miniforge3-$(uname)-$(uname -m).sh -b -p $HOME/miniforge` \n",
-    "    \n",
-    "    Remember to add mamba to the path.   \n",
-    "    \n",
-    "`import os`   \n",
-    "`os.environ[\"PATH\"] += os.pathsep + os.environ[\"HOME\"]+\"/miniforge/bin\"`\n",
-    "  \n",
-    "\n",
-    "</details>"
+    "## Get Started"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "4d1cd3f7-38f0-4606-8b3c-0c5c6dc26fe2",
    "metadata": {},
    "source": [
-    "Next, use mamba to install the tools needed for this analysis: fastqc, multiqc bismark, trim-galore, bedtools, samtools, and metilene. Remember to set the channel to bioconda in order to access the bioinformatics tools."
+    "Use mamba to install the tools needed for this analysis: fastqc, multiqc bismark, trim-galore, bedtools, samtools, and metilene. Remember to set the channel to bioconda in order to access the bioinformatics tools."
    ]
   },
   {