Merge pull request #12 from IHEC/pdf_readme

Add pdf readme files

docs/trackhub_specification.md

@@ -78,7 +78,8 @@ visibility full`
 	shortLabel DG-75.DNase.DG-75
 	longLabel DG-75 DNase DG-75 peaks from NCMLS
 	color 8,104,172
-	subGroups experiment=DNase sample_description=DG-75 analysis_type=HOTSPOT_peak view=Region analysis_group=EMBL-EBI
+	subGroups experiment=DNase sample_description=DG-75 analysis_type=HOTSPOT_peak 
+          view=Region analysis_group=EMBL-EBI
 	metadata ...
 
 	track bpDnaseRegionsBP_U-266_d01DNaseHOTSPOT_peakEMBL-EBI
@@ -88,7 +89,8 @@ visibility full`
 	shortLabel U-266.DNase.U-266
 	longLabel U-266 DNase U-266 peaks from NCMLS
 	color 8,104,172
-	subGroups experiment=DNase sample_description=U-266 analysis_type=HOTSPOT_peak donor_id=U-266 view=Region analysis_group=EMBL-EBI
+	subGroups experiment=DNase sample_description=U-266 analysis_type=HOTSPOT_peak 
+          donor_id=U-266 view=Region analysis_group=EMBL-EBI
 	metadata ...
 
   track signal  
@@ -107,7 +109,8 @@ visibility full`
 	shortLabel DG-75.DNase.DG-75
 	longLabel DG-75 DNase DG-75 signal from NCMLS
 	color 8,104,172
-	subGroups experiment=DNase sample_description=DG-75 analysis_type=wiggler view=Signal analysis_group=EMBL-EBI
+	subGroups experiment=DNase sample_description=DG-75 analysis_type=wiggler 
+          view=Signal analysis_group=EMBL-EBI
 	metadata ...
 
 	track bpDnaseSignalBP_U-266_d01DNasewigglerEMBL-EBIwiggler
@@ -117,7 +120,8 @@ visibility full`
 	shortLabel U-266.DNase.U-266
 	longLabel U-266 DNase U-266 signal from NCMLS
 	color 8,104,172
-	subGroups experiment=DNase sample_description=U-266 analysis_type=wiggler view=Signal analysis_group=EMBL-EBI
+	subGroups experiment=DNase sample_description=U-266 analysis_type=wiggler 
+          view=Signal analysis_group=EMBL-EBI
 	metadata ...
 
 ####Required attributes
@@ -189,11 +193,14 @@ shortLabel C0010K.DNase.Mono
 longLabel C0010K DNase Monocytes peaks (EBI)  
 color 8,104,172  
 subGroups experiment_type=DNase cell_type=CD14-positive,_CD16-negative_classical_monocyte donor_id=C0010K view=Region analysis_group=EBI  
-metadata MOLECULE=genomic_DNA DISEASE=None BIOMATERIAL_TYPE=Primary_cells   SAMPLE_ID=EGAN00001070025 DONOR_ID=C0010K46 DONOR_AGE=60-65 DONOR_HEALTH_STATUS=Healthy   DONOR_SEX=Female DONOR_ETHNICITY=Northern_European CELL_TYPE=CD14-positive,_CD16-negative_classical_monocyte TISSUE_TYPE=Venous_blood LIBRARY_STRATEGY=DNAse-Seq   EXPERIMENT_TYPE=Chromatin_accessibility Experiment_ID=EGAX00001084791   ALIGNMENT_SOFTWARE=BWA ALIGNMENT_SOFTWARE_VERSION=0.5.9 ANALYSIS_SOFTWARE=Hotspot   ANALYSIS_SOFTWARE_VERSION=v3 ANALYSIS_GROUP=EMBL-EBI  
+metadata MOLECULE=genomic_DNA DISEASE=None BIOMATERIAL_TYPE=Primary_cells   
+  SAMPLE_ID=EGAN00001070025 DONOR_ID=C0010K46 DONOR_AGE=60-65 DONOR_HEALTH_STATUS=Healthy   DONOR_SEX=Female 
+  DONOR_ETHNICITY=Northern_European CELL_TYPE=CD14-positive,_CD16-negative_classical_monocyte TISSUE_TYPE=Venous_blood LIBRARY_STRATEGY=DNAse-Seq   EXPERIMENT_TYPE=Chromatin_accessibility Experiment_ID=EGAX00001084791   ALIGNMENT_SOFTWARE=BWA ALIGNMENT_SOFTWARE_VERSION=0.5.9 ANALYSIS_SOFTWARE=Hotspot   ANALYSIS_SOFTWARE_VERSION=v3 ANALYSIS_GROUP=EMBL-EBI  
 
 This is an example of a  metadata suitable for cell line sample:
 
-metadata LINE=BL-2 DIFFERENTIATION_STAGE=B_cell MEDIUM=RPMI_1640_+_10%FBS_+_1%_Glutamine   SEX=Male MOLECULE=genomic_DNA  DISEASE=Sporadic_Burkitt_lymphoma   DISEASE_ONTOLOGY_URI=http://ncimeta.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code=C1336077 BIOMATERIAL_TYPE=Cell_line   SAMPLE_ONTOLOGY_URI=http://www.ebi.ac.uk/efo/EFO_0001639 SAMPLE_ID=ERS333897   LIBRARY_STRATEGY=DNAse-Seq  EXPERIMENT_TYPE=H3K27ac Experiment_ID=EGAX00001084792   ALIGNMENT_SOFTWARE=BWA ALIGNMENT_SOFTWARE_VERSION=0.5.9 ANALYSIS_SOFTWARE=Hotspot   ANALYSIS_SOFTWARE_VERSION=v3 ANALYSIS_GROUP=EMBL-EBI  
+metadata LINE=BL-2 DIFFERENTIATION_STAGE=B_cell 
+  MEDIUM=RPMI_1640_+_10%FBS_+_1%_Glutamine   SEX=Male MOLECULE=genomic_DNA  DISEASE=Sporadic_Burkitt_lymphoma   DISEASE_ONTOLOGY_URI=http://ncimeta.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code=C1336077 BIOMATERIAL_TYPE=Cell_line   SAMPLE_ONTOLOGY_URI=http://www.ebi.ac.uk/efo/EFO_0001639 SAMPLE_ID=ERS333897   LIBRARY_STRATEGY=DNAse-Seq  EXPERIMENT_TYPE=H3K27ac Experiment_ID=EGAX00001084792   ALIGNMENT_SOFTWARE=BWA ALIGNMENT_SOFTWARE_VERSION=0.5.9 ANALYSIS_SOFTWARE=Hotspot   ANALYSIS_SOFTWARE_VERSION=v3 ANALYSIS_GROUP=EMBL-EBI  
 
 This is an example of a metadata suitable for primary tissue sample:
 
@@ -202,7 +209,8 @@ SAMPLE_ONTOLOGY_URI=http://purl.obolibrary.org/obo/CL_0000775
 
 This is an example of a metadata suitable for a primary cell culture sample:
 
-metadata MOLECULE=genomic_DNA DISEASE=None BIOMATERIAL_TYPE=Primary_Cell_Culture CELL_TYPE=macrophage SAMPLE_ID=EGAN00001070028 DONOR_ID=C0010K46 DONOR_AGE=60-65 DONOR_HEALTH_STATUS=Healthy DONOR_SEX=Female DONOR_ETHNICITY=Northern_European CULTURE_CONDITIONS=http://www.blueprint-epigenome.eu/UserFiles/file/Protocols/UCAM_BluePrint_Macrophage.pdf LIBRARY_STRATEGY=DNAse-Seq EXPERIMENT_TYPE=Chromatin_accessibility Experiment_ID=EGAX00001084792 ALIGNMENT_SOFTWARE=BWA ALIGNMENT_SOFTWARE_VERSION=0.5.9 ANALYSIS_SOFTWARE=Hotspot ANALYSIS_SOFTWARE_VERSION=v3 ANALYSIS_GROUP=EMBL-EBI
+metadata MOLECULE=genomic_DNA DISEASE=None BIOMATERIAL_TYPE=Primary_Cell_Culture CELL_TYPE=macrophage SAMPLE_ID=EGAN00001070028 DONOR_ID=C0010K46 DONOR_AGE=60-65 DONOR_HEALTH_STATUS=Healthy DONOR_SEX=Female 
+  DONOR_ETHNICITY=Northern_European CULTURE_CONDITIONS=http://www.blueprint-epigenome.eu/UserFiles/file/Protocols/UCAM_BluePrint_Macrophage.pdf LIBRARY_STRATEGY=DNAse-Seq EXPERIMENT_TYPE=Chromatin_accessibility Experiment_ID=EGAX00001084792 ALIGNMENT_SOFTWARE=BWA ALIGNMENT_SOFTWARE_VERSION=0.5.9 ANALYSIS_SOFTWARE=Hotspot ANALYSIS_SOFTWARE_VERSION=v3 ANALYSIS_GROUP=EMBL-EBI
 SAMPLE_ONTOLOGY_URI=http://purl.obolibrary.org/obo/CL_0000235
 
 

minimum_required_track_types.md

@@ -9,47 +9,47 @@ Please refer to the [tracks generation standards](./tracks_generation.md) for in
 #### ChIP-Seq Histone (H3K*):
 
 
-| Track Type                     | Data Hub Identifier              | Format | Mandatory | Notes |
-|--------------------------------|----------------------------------|--------|-----------|-------|
-| Signal/Coverage                | `signal_unstranded`              | bigWig | ✓         | |
-| Peak calls                     | `peak_calls`                     | bigBed | ✓         | |
+| Track Type                     | Data Hub Identifier              | Format   | Mandatory   | Notes |
+|--------------------------------|----------------------------------|:--------:|:-----------:|---------------------------------------|
+| Signal/Coverage                | `signal_unstranded`              | bigWig   | Y           | |
+| Peak calls                     | `peak_calls`                     | bigBed   | Y           | |
 
 
 ### ChIP-Seq Input:
 
-| Track Type                     | Data Hub Identifier              | Format | Mandatory | Notes |
-|--------------------------------|----------------------------------|--------|-----------|-------|
-| Signal/Coverage                | `signal_unstranded`              | bigWig | ✓         | |
+| Track Type                     | Data Hub Identifier              | Format   | Mandatory   | Notes |
+|--------------------------------|----------------------------------|:--------:|:-----------:|-------|
+| Signal/Coverage                | `signal_unstranded`              | bigWig   | Y           | |
 
 
 ### DNA Methylation:
 
-| Track Type                     | Data Hub Identifier              | Format | Mandatory | Notes |
-|--------------------------------|----------------------------------|--------|-----------|-------|
-| Fractional Methylation Calls   | `methylation_profile`            | bigWig | ✓         | Needs to be formally specified, reports #Cs vs #Ts at each CpG site. See current proposal [here](./Fractional_Methylation_Proposal.md).|
-| Signal/Coverage                | `signal_unstranded` OR `signal_forward`,`signal_reverse` | bigWig |  ✓         | Raw coverage over CpGs as a measure of confidence in Fractional Methtylation Calls. See current proposal [here](./Fractional_Methylation_Proposal.md).|
+| Track Type                 | Data Hub Identifier                  | Format    | Mandatory   | Notes |
+|----------------------------|--------------------------------------|:---------:|:-----------:|----------------------------------|
+| Fractional Methylation Calls | `methylation_profile`              | bigWig    | Y           | Needs to be formally specified, reports #Cs vs #Ts at each CpG site. See current proposal [here](./Fractional_Methylation_Proposal.md).|
+| Signal/Coverage              | `signal_unstranded` OR `signal_forward`, `signal_reverse` | bigWig |  Y         | Raw coverage over CpGs as a measure of confidence in Fractional Methtylation Calls. See current proposal [here](./Fractional_Methylation_Proposal.md).|
 
 
 ### mRNA / total RNA :
 
 #### For strand specific signal:
-| Track Type                     | Data Hub Identifier              | Format | Mandatory | Notes |
-|--------------------------------|----------------------------------|--------|-----------|-------|
-| Signal/Coverage forward strand | `signal_forward`                 | bigWig | ✓        | |
-| Signal/Coverage reverse strand | `signal_reverse`                 | bigWig | ✓        | |
-| RPKM on positive strand        | `rpkm_forward`                   | bigWig |          | Computation needs to be standardized. Proposal available [here](https://github.com/IHEC/ihec-assay-standards/blob/master/RNA_Seq_normalization.md). |
-| RPKM on negative strand        | `rpkm_reverse`                   | bigWig |          | Computation needs to be standardized. Proposal available [here](https://github.com/IHEC/ihec-assay-standards/blob/master/RNA_Seq_normalization.md). |
+| Track Type                     | Data Hub Identifier          | Format   | Mandatory | Notes |
+|--------------------------------|------------------------------|:--------:|:---------:|---------------------------------|
+| Signal/Coverage forward strand | `signal_forward`             | bigWig   | Y         | |
+| Signal/Coverage reverse strand | `signal_reverse`             | bigWig   | Y         | |
+| RPKM on positive strand        | `rpkm_forward`               | bigWig   |           | Computation needs to be standardized. Proposal available [here](https://github.com/IHEC/ihec-assay-standards/blob/master/RNA_Seq_normalization.md). |
+| RPKM on negative strand        | `rpkm_reverse`               | bigWig   |           | Computation needs to be standardized. Proposal available [here](https://github.com/IHEC/ihec-assay-standards/blob/master/RNA_Seq_normalization.md). |
 
 
 
 
 
 #### For single stranded signal:
 
-| Track Type                     | Data Hub Identifier              | Format | Mandatory | Notes |
-|--------------------------------|----------------------------------|--------|-----------|-------|
-| Signal/Coverage                | `signal_unstranded`              | bigWig | ✓         | |
-| RPKM                           | `rpkm_unstranded`                | bigWig |           | Computation needs to be standardized. Proposal available [here](https://github.com/IHEC/ihec-assay-standards/blob/master/RNA_Seq_normalization.md). |
+| Track Type                     | Data Hub Identifier              | Format   | Mandatory | Notes |
+|--------------------------------|----------------------------------|:--------:|:---------:|-------------------------------|
+| Signal/Coverage                | `signal_unstranded`              | bigWig   | Y         | |
+| RPKM                           | `rpkm_unstranded`                | bigWig   |           | Computation needs to be standardized. Proposal available [here](https://github.com/IHEC/ihec-assay-standards/blob/master/RNA_Seq_normalization.md). |
 
 
 
@@ -58,24 +58,24 @@ Please refer to the [tracks generation standards](./tracks_generation.md) for in
 
 ### smRNA-Seq signal: 
 
-| Track Type                     | Data Hub Identifier              | Format | Mandatory | Notes |
-|--------------------------------|----------------------------------|--------|-----------|-------|
-| Signal/Coverage                | `signal_unstranded`              | bigWig | ✓         | |
-| Reads per million miRNA mapped | `reads_per_million_miRNA_mapped` | bigWig |           | Computation needs to be standardized |
+| Track Type                     | Data Hub Identifier               | Format   | Mandatory | Notes |
+|--------------------------------|-----------------------------------|:--------:|:---------:|-------------------------------|
+| Signal/Coverage                | `signal_unstranded`               | bigWig   | Y         |                                      |
+| Reads per million miRNA mapped | `reads_per_million_ miRNA_mapped` | bigWig   |           | Computation needs to be standardized |
 
 
 
 ### Whole Genome Sequencing:
 
-| Track Type                     | Data Hub Identifier              | Format | Mandatory | Notes |
-|--------------------------------|----------------------------------|--------|-----------|-------|
-| Copy Number Variation          | `copy_number_variation`          | bigWig | ✓         | |
+| Track Type                     | Data Hub Identifier              | Format   | Mandatory  | Notes |
+|--------------------------------|----------------------------------|:--------:|:----------:|-------|
+| Copy Number Variation          | `copy_number_variation`          | bigWig   | Y          | |
 
 
 
 ### ATAC-Seq: 
 
-| Track Type                     | Data Hub Identifier              | Format | Mandatory | Notes |
-|--------------------------------|----------------------------------|--------|-----------|-------|
-| Signal/Coverage                | `signal_unstranded`              | bigWig | ✓         | |
-| Peak calls                     | `peak_calls`                     | bigBed | ✓         | |
+| Track Type                     | Data Hub Identifier              | Format   | Mandatory  | Notes |
+|--------------------------------|----------------------------------|:--------:|:----------:|-------|
+| Signal/Coverage                | `signal_unstranded`              | bigWig   | Y          | |
+| Peak calls                     | `peak_calls`                     | bigBed   | Y          | |

scripts/markdown2pdf

@@ -0,0 +1,23 @@
+#!/usr/bin/env bash
+
+SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+DOCS_DIR=$SCRIPT_DIR/../docs
+ROOT_DIR=$SCRIPT_DIR/..
+LATEX_OPTS="--variable=colorlinks"
+
+for m in $DOCS_DIR/*.md; do 
+	p=`echo $m | sed 's/\.md$/.pdf/'`;
+	echo "Converting $m to $p";
+	pandoc -f markdown_github $LATEX_OPTS -o $p $m
+done
+
+for n in $ROOT_DIR/*.md; do
+  if [[ "$n" =~ README\.md$ ]]; then
+    echo "not converting $n"
+  else
+    q=`echo $n | sed 's/\.md$/.pdf/'`;
+    echo "Converting $n to $q";
+    pandoc -f markdown_github $LATEX_OPTS -o $q $n
+  fi
+done
+