Commit 31bbaecb authored by Mark Iskander's avatar Mark Iskander

Updated to bcftools 1.3

parent 283980c4
Pipeline #938 passed with stage
......@@ -15,7 +15,7 @@ Additionality, tools available from toolshed.g2.bx.psu.edu will also be installe
* **freebayes by devteam at 99684adf84de
* **msa_datatypes by iuc at 70227007b991
* **package_bcftools_1_2 by iuc at 70a313a2366f
* **package_bcftools_1_3 by iuc at 43a9aebf3adb
* **package_freebayes_0_9_20_b040236 by devteam at 059e6e3d99cc
* **package_mummer_3_23 by iuc at 9ddc606546c3
* **package_ncurses_5_9 by iuc at 5e1760c773ba
......@@ -35,7 +35,7 @@ Additionality, tools available from toolshed.g2.bx.psu.edu will also be installe
* 'admin@localhost.com' is not created yet.
* ToolShed is currently running
### One script install
### One script install
```bash
......
......@@ -34,7 +34,7 @@
<change_format>
<when format="bcf" input="output_format" value="u" />
<when format="vcf_bgzip" input="output_format" value="z" />
<when format="bcf_bgzip" input="output_format" value="b" />
<when format="bcf_bgzip" input="output_format" value="b" />
</change_format>
</data>
</xml>
......@@ -48,7 +48,7 @@
</xml>
<xml name="requirements">
<requirements>
<requirement type="package" version="1.2">bcftools</requirement>
<requirement type="package" version="1.3">bcftools</requirement>
<requirement type="package" version="0.2.6">tabix</requirement>
</requirements>
</xml>
......
<?xml version="1.0"?>
<tool_dependency>
<package name="bcftools" version="1.2">
<repository name="package_bcftools_1_2" owner="iuc" />
<package name="bcftools" version="1.3">
<repository name="package_bcftools_1_3" owner="iuc" />
</package>
<package name="tabix" version="0.2.6">
<repository name="package_tabix_0_2_6" owner="iuc" />
......
......@@ -34,7 +34,7 @@
<change_format>
<when format="bcf" input="output_format" value="u" />
<when format="vcf_bgzip" input="output_format" value="z" />
<when format="bcf_bgzip" input="output_format" value="b" />
<when format="bcf_bgzip" input="output_format" value="b" />
</change_format>
</data>
</xml>
......@@ -48,7 +48,7 @@
</xml>
<xml name="requirements">
<requirements>
<requirement type="package" version="1.2">bcftools</requirement>
<requirement type="package" version="1.3">bcftools</requirement>
<requirement type="package" version="0.2.6">tabix</requirement>
</requirements>
</xml>
......
......@@ -51,7 +51,7 @@
##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
##bcftools_viewVersion=1.2+htslib-1.2.1
##bcftools_viewVersion=1.3+htslib-1.3
##bcftools_viewCommand=view -O b -o /home/phil/cholera-files-subsample/test/vcf-split/3554-08.bcf.gz
##bcftools_viewCommand=view input.bcf.gz
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown
......
......@@ -11,4 +11,4 @@ capsule_toolshed.g2.bx.psu.edu_package_samtools_1_2_iuc_f6ae3ba3f3c1.tar.gz
capsule_toolshed.g2.bx.psu.edu_regex_find_replace_jjohnson_9ea374bb0350.tar.gz
capsule_toolshed.g2.bx.psu.edu_samtools_mpileup_devteam_aa0ef6f0ee89.tar.gz
capsule_toolshed.g2.bx.psu.edu_freebayes_devteam_99684adf84de.tar.gz
capsule_toolshed.g2.bx.psu.edu_package_bcftools_1_2_iuc_70a313a2366f.tar.gz
capsule_toolshed.g2.bx.psu.edu_package_bcftools_1_3_iuc_43a9aebf3adb.tar.gz
......@@ -32,7 +32,7 @@
<action type="shell_command">git clone https://irida.corefacility.ca/analysis-pipelines/snvphyl-tools.git</action>
<action type="change_directory">snvphyl-tools</action>
<action type="shell_command">git checkout 7aa19843f6b0d350e0c8aa26b8d6407aab20cb45</action>
<action type="change_directory">bcfplugins/bcftools-1.2</action>
<action type="change_directory">bcfplugins/bcftools-1.3</action>
<action type="shell_command">make</action>
<action type="change_directory">../..</action>
<action type="move_directory_files">
......@@ -42,10 +42,10 @@
<action type="set_environment">
<environment_variable action="set_to" name="VCF2PSEUDO">$INSTALL_DIR/snvphyl</environment_variable>
<environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/snvphyl/bcfplugins/bcftools-1.2/htslib-1.2.1</environment_variable>
<environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/snvphyl/bcfplugins/bcftools-1.2</environment_variable>
<environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/snvphyl/bcfplugins/bcftools-1.3/htslib-1.3</environment_variable>
<environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/snvphyl/bcfplugins/bcftools-1.3</environment_variable>
<environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable>
<environment_variable action="set_to" name="BCFTOOLS_PLUGINS">$INSTALL_DIR/snvphyl/bcfplugins/bcftools-1.2/plugins</environment_variable>
<environment_variable action="set_to" name="BCFTOOLS_PLUGINS">$INSTALL_DIR/snvphyl/bcfplugins/bcftools-1.3/plugins</environment_variable>
</action>
</actions>
......
......@@ -2,7 +2,7 @@
<description>combine freebayes and mpileup files for use by vcf2pseudoalignment</description>
<requirements>
<requirement type="package" version="1.6.1-dev">snvphyl</requirement>
<requirement type="package" version="1.2">bcftools</requirement>
<requirement type="package" version="1.3">bcftools</requirement>
</requirements>
<stdio>
<exit_code range="1:" level="fatal" description="Unknown error has occurred"/>
......
......@@ -3,7 +3,7 @@
<package name="snvphyl" version="1.6.1-dev">
<repository name="package_snvphyl_1_6_1_dev" owner="nml" />
</package>
<package name="bcftools" version="1.2">
<repository name="package_bcftools_1_2" owner="iuc"/>
<package name="bcftools" version="1.3">
<repository name="package_bcftools_1_3" owner="iuc"/>
</package>
</tool_dependency>
......@@ -2,7 +2,7 @@
<description>create a pseudo alignment from multiple VCFs files</description>
<requirements>
<requirement type="package" version="1.6.1-dev">snvphyl</requirement>
<requirement type="package" version="1.2">bcftools</requirement>
<requirement type="package" version="1.3">bcftools</requirement>
</requirements>
<stdio>
<exit_code range="1:" level="fatal" description="Unknown error has occurred"/>
......
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