diff --git a/docs_jupyter/how_to_convert_fastq_from_sra.ipynb b/docs_jupyter/how_to_convert_fastq_from_sra.ipynb index 739249d..86758e7 100644 --- a/docs_jupyter/how_to_convert_fastq_from_sra.ipynb +++ b/docs_jupyter/how_to_convert_fastq_from_sra.ipynb @@ -51,7 +51,7 @@ "Metadata folder: /home/bnt4me/virginia/repos/geofetch/docs_jupyter/red_algae\n", "Trying GSE67303 (not a file) as accession...\n", "Skipped 0 accessions. Starting now.\n", - "\u001b[38;5;200mProcessing accession 1 of 1: 'GSE67303'\u001b[0m\n", + "\u001B[38;5;200mProcessing accession 1 of 1: 'GSE67303'\u001B[0m\n", "Processed 4 samples.\n", "Expanding metadata list...\n", "Found SRA Project accession: SRP056574\n", @@ -100,8 +100,8 @@ "Finished processing 1 accession(s)\n", "Cleaning soft files ...\n", "Creating complete project annotation sheets and config file...\n", - "\u001b[92mSample annotation sheet: /home/bnt4me/virginia/repos/geofetch/docs_jupyter/red_algae/GSE67303_PEP/GSE67303_PEP_raw.csv . Saved!\u001b[0m\n", - "\u001b[92mFile has been saved successfully\u001b[0m\n", + "\u001B[92mSample annotation sheet: /home/bnt4me/virginia/repos/geofetch/docs_jupyter/red_algae/GSE67303_PEP/GSE67303_PEP_raw.csv . Saved!\u001B[0m\n", + "\u001B[92mFile has been saved successfully\u001B[0m\n", " Config file: /home/bnt4me/virginia/repos/geofetch/docs_jupyter/red_algae/GSE67303_PEP/GSE67303_PEP.yaml\n" ] } @@ -128,10 +128,10 @@ "name": "stdout", "output_type": "stream", "text": [ - "\u001b[0m\u001b[01;34mbuild\u001b[0m python-usage.ipynb \u001b[01;34mSRR1930184\u001b[0m\n", - "\u001b[01;34mcode\u001b[0m raw-data-downloading.ipynb \u001b[01;34mSRR1930185\u001b[0m\n", - "how_to_fastq_from_sra.ipynb \u001b[01;34mred_algae\u001b[0m \u001b[01;34mSRR1930186\u001b[0m\n", - "processed-data-downloading.ipynb \u001b[01;34mSRR1930183\u001b[0m\n" + "\u001B[0m\u001B[01;34mbuild\u001B[0m python-usage.ipynb \u001B[01;34mSRR1930184\u001B[0m\n", + "\u001B[01;34mcode\u001B[0m raw-data-downloading.ipynb \u001B[01;34mSRR1930185\u001B[0m\n", + "how_to_fastq_from_sra.ipynb \u001B[01;34mred_algae\u001B[0m \u001B[01;34mSRR1930186\u001B[0m\n", + "processed-data-downloading.ipynb \u001B[01;34mSRR1930183\u001B[0m\n" ] } ], @@ -336,7 +336,7 @@ "outputs": [], "source": [ "# Unfortunately you have to pull gefetch folder from github, and set CODE variable:\n", - "mkdir code && cd code && git pull https://github.com/pepkit/geofetch.git && export CODE=`pwd` && cd .." + "mkdir code && cd code && git clone https://github.com/pepkit/geofetch.git && export CODE=`pwd` && cd .." ] }, { @@ -349,10 +349,10 @@ "name": "stdout", "output_type": "stream", "text": [ - "\u001b[0m\u001b[01;34mbuild\u001b[0m processed-data-downloading.ipynb \u001b[01;34mSRR1930183\u001b[0m\n", - "\u001b[01;34mcode\u001b[0m python-usage.ipynb \u001b[01;34mSRR1930184\u001b[0m\n", - "\u001b[01;34mfq_folder\u001b[0m raw-data-downloading.ipynb \u001b[01;34mSRR1930185\u001b[0m\n", - "how_to_fastq_from_sra.ipynb \u001b[01;34mred_algae\u001b[0m \u001b[01;34mSRR1930186\u001b[0m\n" + "\u001B[0m\u001B[01;34mbuild\u001B[0m processed-data-downloading.ipynb \u001B[01;34mSRR1930183\u001B[0m\n", + "\u001B[01;34mcode\u001B[0m python-usage.ipynb \u001B[01;34mSRR1930184\u001B[0m\n", + "\u001B[01;34mfq_folder\u001B[0m raw-data-downloading.ipynb \u001B[01;34mSRR1930185\u001B[0m\n", + "how_to_fastq_from_sra.ipynb \u001B[01;34mred_algae\u001B[0m \u001B[01;34mSRR1930186\u001B[0m\n" ] } ], @@ -379,7 +379,7 @@ "output_type": "stream", "text": [ "looper 1.4.3\n", - "\u001b[0m\n" + "\u001B[0m\n" ] } ], @@ -397,7 +397,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "\u001b[0m\u001b[01;34mGSE67303_PEP\u001b[0m\n" + "\u001B[0m\u001B[01;34mGSE67303_PEP\u001B[0m\n" ] } ], @@ -421,7 +421,7 @@ "Using amendments: sra_convert\n", "Activating compute package 'local'\n", "Pipestat compatible: False\n", - "\u001b[36m## [1 of 4] sample: cm_bluelight_rep1; pipeline: sra_convert\u001b[0m\n", + "\u001B[36m## [1 of 4] sample: cm_bluelight_rep1; pipeline: sra_convert\u001B[0m\n", "Writing script to /home/bnt4me/virginia/repos/geofetch/docs_jupyter/submission/sra_convert_cm_bluelight_rep1.sub\n", "Job script (n=1; 0.06Gb): ./submission/sra_convert_cm_bluelight_rep1.sub\n", "Compute node: bnt4me-Precision-5560\n", @@ -481,7 +481,7 @@ "* Total elapsed time (all runs): 0:00:02\n", "* Peak memory (this run): 0.0803 GB\n", "* Pipeline completed time: 2023-08-01 13:06:44\n", - "\u001b[36m## [2 of 4] sample: cm_bluelight_rep2; pipeline: sra_convert\u001b[0m\n", + "\u001B[36m## [2 of 4] sample: cm_bluelight_rep2; pipeline: sra_convert\u001B[0m\n", "Writing script to /home/bnt4me/virginia/repos/geofetch/docs_jupyter/submission/sra_convert_cm_bluelight_rep2.sub\n", "Job script (n=1; 0.04Gb): ./submission/sra_convert_cm_bluelight_rep2.sub\n", "Compute node: bnt4me-Precision-5560\n", @@ -541,7 +541,7 @@ "* Total elapsed time (all runs): 0:00:02\n", "* Peak memory (this run): 0.0118 GB\n", "* Pipeline completed time: 2023-08-01 13:06:47\n", - "\u001b[36m## [3 of 4] sample: cm_darkness_rep1; pipeline: sra_convert\u001b[0m\n", + "\u001B[36m## [3 of 4] sample: cm_darkness_rep1; pipeline: sra_convert\u001B[0m\n", "Writing script to /home/bnt4me/virginia/repos/geofetch/docs_jupyter/submission/sra_convert_cm_darkness_rep1.sub\n", "Job script (n=1; 0.09Gb): ./submission/sra_convert_cm_darkness_rep1.sub\n", "Compute node: bnt4me-Precision-5560\n", @@ -601,7 +601,7 @@ "* Total elapsed time (all runs): 0:00:03\n", "* Peak memory (this run): 0.0793 GB\n", "* Pipeline completed time: 2023-08-01 13:06:50\n", - "\u001b[36m## [4 of 4] sample: cm_darkness_rep2; pipeline: sra_convert\u001b[0m\n" + "\u001B[36m## [4 of 4] sample: cm_darkness_rep2; pipeline: sra_convert\u001B[0m\n" ] }, { @@ -672,7 +672,7 @@ "Samples valid for job generation: 4 of 4\n", "Commands submitted: 4 of 4\n", "Jobs submitted: 4\n", - "\u001b[0m\n" + "\u001B[0m\n" ] } ],