Add Picard

docs/software/picard.md

@@ -0,0 +1,162 @@
+# Picard
+
+'Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF'
+([source: the Picard documentation](https://broadinstitute.github.io/picard/index.html)).
+
+## Usage
+
+Load the `bioinfo-tools` [module](../cluster_guides/modules.md) first:
+
+```bash
+module load bioinfo-tools
+```
+
+Then search for you favorite Picard version:
+
+```bash
+module spider picard
+```
+
+???- question "How does this look like?"
+
+    Your output will be similar to this:
+
+    ```bash
+    [richel@rackham2 ~]$ module spider picard
+
+    ----------------------------------------------------------------------------
+      picard:
+    ----------------------------------------------------------------------------
+         Versions:
+            picard/1.92
+            picard/1.118
+            picard/1.141
+            picard/2.0.1
+            picard/2.10.3
+            picard/2.19.2
+            picard/2.20.4
+            picard/2.23.4
+            picard/2.27.5
+            picard/3.1.1
+
+    ----------------------------------------------------------------------------
+      For detailed information about a specific "picard" package (including how to l
+    oad the modules) use the module's full name.
+      Note that names that have a trailing (E) are extensions provided by other modu
+    les.
+      For example:
+
+         $ module spider picard/3.1.1
+    ----------------------------------------------------------------------------
+    ```
+
+Then load your favorite version:
+
+
+```bash
+module load picard/3.1.1
+```
+
+???- question "How does this look like?"
+
+    Your output will be similar to this:
+
+    ```bash
+    [richel@rackham2 ~]$ module load picard/3.1.1
+    picard/3.1.1: java -jar $PICARD command ...
+    ```
+
+Read up on how to use Picard:
+
+```bash
+module help picard/3.1.1
+```
+
+???- question "How does this look like?"
+
+    Your output will be similar to this:
+
+    ```
+    [richel@rackham2 ~]$ module help picard/3.1.1
+
+    ----------------------------------------------------------------------- Module Specific Help for "picard/3.1.1" -----------------------------------------------------------------------
+	    picard - use picard/3.1.1
+
+        Version 3.1.1
+
+    Usage:
+
+        java -jar $PICARD command ...
+
+    or
+
+        java -jar $PICARD_ROOT/picard.jar command ...
+
+    where 'command' is the desired Picard command, and ... are the desired further arguments.
+
+    ```
+
+Here is an example of using Picard to test if a file is a valid BAM/CRAM/SAM file:
+
+```bash
+java -jar $PICARD ValidateSamFile --INPUT my_file.bam
+```
+
+???- question "How does this look like?"
+
+    First, download an example BAM file from the Picard GitHub repository:
+
+    ```bash
+    [richel@rackham2 ~]$ wget https://github.com/broadinstitute/picard/raw/master/testdata/picard/flow/reads/input/sample_mc.bam
+
+    --2024-08-05 09:16:40--  https://github.com/broadinstitute/picard/raw/master/testdata/picard/flow/reads/input/sample_mc.bam
+    Resolving github.com (github.com)... 140.82.121.3
+    Connecting to github.com (github.com)|140.82.121.3|:443... connected.
+    HTTP request sent, awaiting response... 302 Found
+    Location: https://raw.githubusercontent.com/broadinstitute/picard/master/testdata/picard/flow/reads/input/sample_mc.bam [following]
+    --2024-08-05 09:16:40--  https://raw.githubusercontent.com/broadinstitute/picard/master/testdata/picard/flow/reads/input/sample_mc.bam
+    Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.109.133, 185.199.108.133, 185.199.110.133, ...
+    Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.109.133|:443... connected.
+    HTTP request sent, awaiting response... 200 OK
+    Length: 117715 (115K) [application/octet-stream]
+    Saving to: ‘sample_mc.bam’
+
+    100%[=============================================================================================================================================>] 117,715     --.-K/s   in 0.001s  
+
+    2024-08-05 09:16:41 (171 MB/s) - ‘sample_mc.bam’ saved [117715/117715]
+    ```
+
+    Your output will be similar to this, when using that valid BAM file:
+
+    ```bash
+    [richel@rackham2 ~]$ java -jar $PICARD ValidateSamFile --INPUT sample_mc.bam 
+    Aug 05, 2024 9:16:47 AM com.intel.gkl.NativeLibraryLoader load
+    INFO: Loading libgkl_compression.so from jar:file:/sw/bioinfo/picard/3.1.1/rackham/picard.jar!/com/intel/gkl/native/libgkl_compression.so
+    [Mon Aug 05 09:16:47 CEST 2024] ValidateSamFile --INPUT sample_mc.bam --MODE VERBOSE --MAX_OUTPUT 100 --IGNORE_WARNINGS false --VALIDATE_INDEX true --INDEX_VALIDATION_STRINGENCY EXHAUSTIVE --IS_BISULFITE_SEQUENCED false --MAX_OPEN_TEMP_FILES 8000 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
+    [Mon Aug 05 09:16:47 CEST 2024] Executing as richel@rackham2.uppmax.uu.se on Linux 3.10.0-1160.119.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 17+35-2724; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.1.1
+    WARNING	2024-08-05 09:16:47	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
+    No errors found
+    [Mon Aug 05 09:16:48 CEST 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.01 minutes.
+    Runtime.totalMemory()=2181038080
+    [richel@rackham2 ~]$ 
+    ```
+
+    Your output will be similar to this, when using an invalid file,
+    such as an R script file:
+
+    ```bash
+    [richel@rackham2 ~]$ java -jar $PICARD ValidateSamFile --INPUT app.R 
+    Aug 05, 2024 9:13:20 AM com.intel.gkl.NativeLibraryLoader load
+    INFO: Loading libgkl_compression.so from jar:file:/sw/bioinfo/picard/3.1.1/rackham/picard.jar!/com/intel/gkl/native/libgkl_compression.so
+    [Mon Aug 05 09:13:20 CEST 2024] ValidateSamFile --INPUT app.R --MODE VERBOSE --MAX_OUTPUT 100 --IGNORE_WARNINGS false --VALIDATE_INDEX true --INDEX_VALIDATION_STRINGENCY EXHAUSTIVE --IS_BISULFITE_SEQUENCED false --MAX_OPEN_TEMP_FILES 8000 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
+    [Mon Aug 05 09:13:21 CEST 2024] Executing as richel@rackham2.uppmax.uu.se on Linux 3.10.0-1160.119.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 17+35-2724; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.1.1
+    WARNING	2024-08-05 09:13:21	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
+    ERROR::MISSING_READ_GROUP:Read groups is empty
+    SAMFormatException on record 01
+    ERROR	2024-08-05 09:13:21	ValidateSamFile	SAMFormatException on record 01
+    [Mon Aug 05 09:13:21 CEST 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.01 minutes.
+    Runtime.totalMemory()=2181038080
+    To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
+    ```
+
+