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Merge pull request #143 from lukenoaa/master
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Added variable for tourmaline path to notebooks, added snakemake log files to .gitignore
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@lukenoaa
lukenoaa authored Aug 14, 2024
2 parents e928a3a + 2bdbd0c commit a81619c
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2 changes: 2 additions & 0 deletions .gitignore
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# Ignore Snakemake log files
logs/*.log
Empty file removed 01-imported/.gitignore
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200 changes: 178 additions & 22 deletions notebooks/tourmaline_meta_analysis.ipynb
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Expand Up @@ -26,7 +26,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 1,
"id": "interstate-wrestling",
"metadata": {},
"outputs": [],
Expand All @@ -47,15 +47,33 @@
"## Set file paths"
]
},
{
"cell_type": "markdown",
"id": "eadf279b",
"metadata": {},
"source": [
"**The value of `tourmdir` should be changed if this notebook is not being run from its original location in the `notebooks` directory.**"
]
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 7,
"id": "3f259b06",
"metadata": {},
"outputs": [],
"source": [
"tourmdir = '..'"
]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "sustainable-round",
"metadata": {},
"outputs": [],
"source": [
"dir_analysis1 = '../meta-analysis/analysis1'\n",
"dir_analysis2 = '../meta-analysis/analysis2'"
"dir_analysis1 = '%s/meta-analysis/analysis1' % tourmdir\n",
"dir_analysis2 = '%s/meta-analysis/analysis2' % tourmdir"
]
},
{
Expand All @@ -76,34 +94,172 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 3,
"id": "fancy-soccer",
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Cloning into 'tourmaline'...\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Removed:\n",
"00-data/fastq/Sample_134723_R2.fastq.gz\n",
"00-data/fastq/Sample_134722_R1.fastq.gz\n",
"00-data/fastq/Sample_134789_R2.fastq.gz\n",
"00-data/fastq/Sample_134719_R1.fastq.gz\n",
"00-data/fastq/Sample_134768_R2.fastq.gz\n",
"00-data/fastq/Sample_134718_R2.fastq.gz\n",
"00-data/fastq/Sample_134771_R2.fastq.gz\n",
"00-data/fastq/Sample_134790_R2.fastq.gz\n",
"00-data/fastq/Sample_134778_R2.fastq.gz\n",
"00-data/fastq/Sample_134767_R2.fastq.gz\n",
"00-data/fastq/Sample_134717_R2.fastq.gz\n",
"00-data/fastq/Sample_134716_R1.fastq.gz\n",
"00-data/fastq/Sample_134772_R2.fastq.gz\n",
"00-data/fastq/Sample_134777_R2.fastq.gz\n",
"00-data/fastq/Sample_134721_R1.fastq.gz\n",
"00-data/fastq/Sample_134720_R2.fastq.gz\n",
"00-data/fastq/Sample_134778_R1.fastq.gz\n",
"00-data/fastq/Sample_134771_R1.fastq.gz\n",
"00-data/fastq/Sample_134790_R1.fastq.gz\n",
"00-data/fastq/Sample_134789_R1.fastq.gz\n",
"00-data/fastq/Sample_134719_R2.fastq.gz\n",
"00-data/fastq/Sample_134768_R1.fastq.gz\n",
"00-data/fastq/Sample_134718_R1.fastq.gz\n",
"00-data/fastq/Sample_134723_R1.fastq.gz\n",
"00-data/fastq/Sample_134722_R2.fastq.gz\n",
"00-data/fastq/Sample_134721_R2.fastq.gz\n",
"00-data/fastq/Sample_134720_R1.fastq.gz\n",
"00-data/fastq/Sample_134777_R1.fastq.gz\n",
"00-data/fastq/Sample_134772_R1.fastq.gz\n",
"00-data/fastq/Sample_134767_R1.fastq.gz\n",
"00-data/fastq/Sample_134717_R1.fastq.gz\n",
"00-data/fastq/Sample_134716_R2.fastq.gz\n",
"00-data/fastq\n",
"00-data/manifest_pe.csv\n",
"00-data/manifest_se.csv\n",
"00-data/metadata.tsv\n",
"00-data/repseqs_to_filter_dada2-pe.tsv\n",
"00-data/repseqs_to_filter_dada2-se.tsv\n",
"00-data/repseqs_to_filter_deblur-se.tsv\n",
"00-data/samples_to_filter_dada2-pe.tsv\n",
"00-data/samples_to_filter_dada2-se.tsv\n",
"00-data/samples_to_filter_deblur-se.tsv\n",
"Copied:\n",
"../../../config.yaml -> config.yaml\n",
"../../../00-data/manifest_pe.csv -> 00-data/manifest_pe.csv\n",
"../../../00-data/manifest_se.csv -> 00-data/manifest_se.csv\n",
"../../../00-data/metadata.tsv -> 00-data/metadata.tsv\n",
"../../../00-data/repseqs_to_filter_dada2-pe.tsv -> 00-data/repseqs_to_filter_dada2-pe.tsv\n",
"../../../00-data/repseqs_to_filter_dada2-se.tsv -> 00-data/repseqs_to_filter_dada2-se.tsv\n",
"../../../00-data/repseqs_to_filter_deblur-se.tsv -> 00-data/repseqs_to_filter_deblur-se.tsv\n",
"../../../01-imported/refseqs.qza -> 01-imported/refseqs.qza\n",
"../../../01-imported/reftax.qza -> 01-imported/reftax.qza\n"
]
}
],
"source": [
"%%bash\n",
"cd ../meta-analysis/analysis1\n",
"git clone https://github.com/aomlomics/tourmaline\n",
"cd tourmaline\n",
"./scripts/initialize_dir_from_existing_tourmaline_dir.sh ../../..\n",
"cp ../metadata.tsv 00-data\n",
"cp ../manifest_* 00-data"
"cp ../manifest_* 00-data\n",
"cp ../../../01-imported/silva-138-99-seqs-515-806.qza 01-imported\n",
"cp ../../../01-imported/silva-138-99-tax-515-806.qza 01-imported"
]
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 4,
"id": "manual-linux",
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Cloning into 'tourmaline'...\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Removed:\n",
"00-data/fastq/Sample_134723_R2.fastq.gz\n",
"00-data/fastq/Sample_134722_R1.fastq.gz\n",
"00-data/fastq/Sample_134789_R2.fastq.gz\n",
"00-data/fastq/Sample_134719_R1.fastq.gz\n",
"00-data/fastq/Sample_134768_R2.fastq.gz\n",
"00-data/fastq/Sample_134718_R2.fastq.gz\n",
"00-data/fastq/Sample_134771_R2.fastq.gz\n",
"00-data/fastq/Sample_134790_R2.fastq.gz\n",
"00-data/fastq/Sample_134778_R2.fastq.gz\n",
"00-data/fastq/Sample_134767_R2.fastq.gz\n",
"00-data/fastq/Sample_134717_R2.fastq.gz\n",
"00-data/fastq/Sample_134716_R1.fastq.gz\n",
"00-data/fastq/Sample_134772_R2.fastq.gz\n",
"00-data/fastq/Sample_134777_R2.fastq.gz\n",
"00-data/fastq/Sample_134721_R1.fastq.gz\n",
"00-data/fastq/Sample_134720_R2.fastq.gz\n",
"00-data/fastq/Sample_134778_R1.fastq.gz\n",
"00-data/fastq/Sample_134771_R1.fastq.gz\n",
"00-data/fastq/Sample_134790_R1.fastq.gz\n",
"00-data/fastq/Sample_134789_R1.fastq.gz\n",
"00-data/fastq/Sample_134719_R2.fastq.gz\n",
"00-data/fastq/Sample_134768_R1.fastq.gz\n",
"00-data/fastq/Sample_134718_R1.fastq.gz\n",
"00-data/fastq/Sample_134723_R1.fastq.gz\n",
"00-data/fastq/Sample_134722_R2.fastq.gz\n",
"00-data/fastq/Sample_134721_R2.fastq.gz\n",
"00-data/fastq/Sample_134720_R1.fastq.gz\n",
"00-data/fastq/Sample_134777_R1.fastq.gz\n",
"00-data/fastq/Sample_134772_R1.fastq.gz\n",
"00-data/fastq/Sample_134767_R1.fastq.gz\n",
"00-data/fastq/Sample_134717_R1.fastq.gz\n",
"00-data/fastq/Sample_134716_R2.fastq.gz\n",
"00-data/fastq\n",
"00-data/manifest_pe.csv\n",
"00-data/manifest_se.csv\n",
"00-data/metadata.tsv\n",
"00-data/repseqs_to_filter_dada2-pe.tsv\n",
"00-data/repseqs_to_filter_dada2-se.tsv\n",
"00-data/repseqs_to_filter_deblur-se.tsv\n",
"00-data/samples_to_filter_dada2-pe.tsv\n",
"00-data/samples_to_filter_dada2-se.tsv\n",
"00-data/samples_to_filter_deblur-se.tsv\n",
"Copied:\n",
"../../../config.yaml -> config.yaml\n",
"../../../00-data/manifest_pe.csv -> 00-data/manifest_pe.csv\n",
"../../../00-data/manifest_se.csv -> 00-data/manifest_se.csv\n",
"../../../00-data/metadata.tsv -> 00-data/metadata.tsv\n",
"../../../00-data/repseqs_to_filter_dada2-pe.tsv -> 00-data/repseqs_to_filter_dada2-pe.tsv\n",
"../../../00-data/repseqs_to_filter_dada2-se.tsv -> 00-data/repseqs_to_filter_dada2-se.tsv\n",
"../../../00-data/repseqs_to_filter_deblur-se.tsv -> 00-data/repseqs_to_filter_deblur-se.tsv\n",
"../../../01-imported/refseqs.qza -> 01-imported/refseqs.qza\n",
"../../../01-imported/reftax.qza -> 01-imported/reftax.qza\n"
]
}
],
"source": [
"%%bash\n",
"cd ../meta-analysis/analysis2\n",
"git clone https://github.com/aomlomics/tourmaline\n",
"cd tourmaline\n",
"./scripts/initialize_dir_from_existing_tourmaline_dir.sh ../../..\n",
"cp ../metadata.tsv 00-data\n",
"cp ../manifest_* 00-data"
"cp ../manifest_* 00-data\n",
"cp ../../../01-imported/silva-138-99-seqs-515-806.qza 01-imported\n",
"cp ../../../01-imported/silva-138-99-tax-515-806.qza 01-imported"
]
},
{
Expand All @@ -127,33 +283,33 @@
"id": "helpful-snapshot",
"metadata": {},
"source": [
"Each commands below will take ~5 minutes to complete. You will not see any output until the command is finished."
"Run the two commands below from your Terminal (i.e., outside of this notebook). Each command will take ~5 minutes to complete."
]
},
{
"cell_type": "code",
"execution_count": null,
"cell_type": "markdown",
"id": "cathedral-professor",
"metadata": {
"scrolled": true
},
"outputs": [],
"source": [
"%%bash\n",
"```bash\n",
"conda activate snakemake\n",
"cd ../meta-analysis/analysis1/tourmaline\n",
"snakemake dada2_pe_report_unfiltered"
"snakemake --use-conda dada2_pe_report_unfiltered --cores 4\n",
"```"
]
},
{
"cell_type": "code",
"execution_count": null,
"cell_type": "markdown",
"id": "brazilian-skating",
"metadata": {},
"outputs": [],
"source": [
"%%bash\n",
"```bash\n",
"conda activate snakemake\n",
"cd ../meta-analysis/analysis2/tourmaline\n",
"snakemake dada2_pe_report_unfiltered"
"snakemake --use-conda dada2_pe_report_unfiltered --cores 4\n",
"```"
]
},
{
Expand Down Expand Up @@ -365,7 +521,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.13"
"version": "3.8.16"
}
},
"nbformat": 4,
Expand Down
78 changes: 45 additions & 33 deletions notebooks/tourmaline_python_notebook.ipynb
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