From e709bbd984007cf86032693e6549985c1c81c7fe Mon Sep 17 00:00:00 2001
From: Jingchao Zhang <zhang@unl.edu>
Date: Wed, 25 Sep 2019 14:45:20 -0500
Subject: [PATCH] moved things under Applications
---
.../Application_Specific_Guides}/Jupyter.md | 0
.../allinea_profiling_and_debugging/_index.md | 0
.../allinea_performance_reports/_index.md | 0
.../blast_with_allinea_performance_reports.md | 0
...lammps_with_allinea_performance_reports.md | 0
.../ray_with_allinea_performance_reports.md | 0
...using_allinea_forge_via_reverse_connect.md | 0
.../bioinformatics_tools/_index.md | 0
.../alignment_tools/_index.md | 0
.../alignment_tools/blast/_index.md | 0
.../blast/create_local_blast_database.md | 0
.../blast/running_blast_alignment.md | 0
.../alignment_tools/blat.md | 0
.../alignment_tools/bowtie.md | 0
.../alignment_tools/bowtie2.md | 0
.../alignment_tools/bwa/_index.md | 0
.../bwa/running_bwa_commands.md | 0
.../alignment_tools/clustal_omega.md | 0
.../alignment_tools/tophat_tophat2.md | 0
.../bioinformatics_tools/biodata_module.md | 0
.../data_manipulation_tools/_index.md | 0
.../bamtools/_index.md | 0
.../bamtools/running_bamtools_commands.md | 0
.../samtools/_index.md | 0
.../samtools/running_samtools_commands.md | 0
.../data_manipulation_tools/sratoolkit.md | 0
.../de_novo_assembly_tools/_index.md | 0
.../de_novo_assembly_tools/oases.md | 0
.../de_novo_assembly_tools/ray.md | 0
.../de_novo_assembly_tools/soapdenovo2.md | 0
.../de_novo_assembly_tools/trinity/_index.md | 0
.../running_trinity_in_multiple_steps.md | 0
.../de_novo_assembly_tools/velvet/_index.md | 0
.../running_velvet_with_paired_end_data.md | 0
...vet_with_single_end_and_paired_end_data.md | 0
.../running_velvet_with_single_end_data.md | 0
.../downloading_sra_data_from_ncbi.md | 0
.../pre_processing_tools/_index.md | 0
.../pre_processing_tools/cutadapt.md | 0
.../pre_processing_tools/prinseq.md | 0
.../pre_processing_tools/scythe.md | 0
.../pre_processing_tools/sickle.md | 0
.../pre_processing_tools/tagcleaner.md | 0
.../bioinformatics_tools/qiime.md | 0
.../reference_based_assembly_tools/_index.md | 0
.../cufflinks.md | 0
.../_index.md | 0
.../cap3.md | 0
.../cd_hit.md | 0
.../dmtcp_checkpointing.md | 0
.../fortran_c_on_hcc.md | 0
.../mpi_jobs_on_hcc.md | 0
.../running_gaussian_at_hcc.md | 0
.../running_matlab_parallel_server.md | 0
...unning_ocean_land_atmosphere_model_olam.md | 0
.../running_theano.md | 0
.../available_software_for_crane.md | 0
.../available_software_for_rhino.md | 0
.../Using_Modules}/module_commands.md | 0
.../compiling_an_openmp_application.md | 0
.../installing_perl_modules.md | 0
.../using_anaconda_package_manager.md | 0
.../using_singularity.md | 0
content/Applications/_index.md | 9 +++++++
content/guides/running_applications/_index.md | 7 -----
.../compiling_source_code/_index.md | 26 -------------------
66 files changed, 9 insertions(+), 33 deletions(-)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/Jupyter.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/allinea_profiling_and_debugging/_index.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/allinea_profiling_and_debugging/allinea_performance_reports/_index.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/allinea_profiling_and_debugging/allinea_performance_reports/blast_with_allinea_performance_reports.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/allinea_profiling_and_debugging/allinea_performance_reports/lammps_with_allinea_performance_reports.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/allinea_profiling_and_debugging/allinea_performance_reports/ray_with_allinea_performance_reports.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/allinea_profiling_and_debugging/using_allinea_forge_via_reverse_connect.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/_index.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/alignment_tools/_index.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/alignment_tools/blast/_index.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/alignment_tools/blast/create_local_blast_database.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/alignment_tools/blat.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/alignment_tools/bowtie.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/alignment_tools/bowtie2.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/alignment_tools/bwa/_index.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/alignment_tools/bwa/running_bwa_commands.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/alignment_tools/clustal_omega.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/alignment_tools/tophat_tophat2.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/biodata_module.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/data_manipulation_tools/_index.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/data_manipulation_tools/bamtools/_index.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/data_manipulation_tools/bamtools/running_bamtools_commands.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/data_manipulation_tools/samtools/_index.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/data_manipulation_tools/samtools/running_samtools_commands.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/data_manipulation_tools/sratoolkit.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/de_novo_assembly_tools/_index.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/de_novo_assembly_tools/oases.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/de_novo_assembly_tools/ray.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/de_novo_assembly_tools/soapdenovo2.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/de_novo_assembly_tools/trinity/_index.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/de_novo_assembly_tools/trinity/running_trinity_in_multiple_steps.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/de_novo_assembly_tools/velvet/_index.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/de_novo_assembly_tools/velvet/running_velvet_with_paired_end_data.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/de_novo_assembly_tools/velvet/running_velvet_with_single_end_and_paired_end_data.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/de_novo_assembly_tools/velvet/running_velvet_with_single_end_data.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/downloading_sra_data_from_ncbi.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/pre_processing_tools/_index.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/pre_processing_tools/cutadapt.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/pre_processing_tools/prinseq.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/pre_processing_tools/scythe.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/pre_processing_tools/sickle.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/pre_processing_tools/tagcleaner.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/qiime.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/reference_based_assembly_tools/_index.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/reference_based_assembly_tools/cufflinks.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/removing_detecting_redundant_sequences/_index.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/removing_detecting_redundant_sequences/cap3.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/bioinformatics_tools/removing_detecting_redundant_sequences/cd_hit.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/dmtcp_checkpointing.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/fortran_c_on_hcc.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/mpi_jobs_on_hcc.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/running_gaussian_at_hcc.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/running_matlab_parallel_server.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/running_ocean_land_atmosphere_model_olam.md (100%)
rename content/{guides/running_applications => Applications/Application_Specific_Guides}/running_theano.md (100%)
rename content/{guides/running_applications => Applications/Using_Modules}/available_software_for_crane.md (100%)
rename content/{guides/running_applications => Applications/Using_Modules}/available_software_for_rhino.md (100%)
rename content/{guides/running_applications => Applications/Using_Modules}/module_commands.md (100%)
rename content/{guides/running_applications/compiling_source_code => Applications/Using_Your_Own_Software}/compiling_an_openmp_application.md (100%)
rename content/{guides/running_applications => Applications/Using_Your_Own_Software}/installing_perl_modules.md (100%)
rename content/{guides/running_applications => Applications/Using_Your_Own_Software}/using_anaconda_package_manager.md (100%)
rename content/{guides/running_applications => Applications/Using_Your_Own_Software}/using_singularity.md (100%)
create mode 100644 content/Applications/_index.md
delete mode 100644 content/guides/running_applications/_index.md
delete mode 100644 content/guides/running_applications/compiling_source_code/_index.md
diff --git a/content/guides/running_applications/Jupyter.md b/content/Applications/Application_Specific_Guides/Jupyter.md
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rename from content/guides/running_applications/Jupyter.md
rename to content/Applications/Application_Specific_Guides/Jupyter.md
diff --git a/content/guides/running_applications/allinea_profiling_and_debugging/_index.md b/content/Applications/Application_Specific_Guides/allinea_profiling_and_debugging/_index.md
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diff --git a/content/guides/running_applications/allinea_profiling_and_debugging/allinea_performance_reports/_index.md b/content/Applications/Application_Specific_Guides/allinea_profiling_and_debugging/allinea_performance_reports/_index.md
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rename from content/guides/running_applications/allinea_profiling_and_debugging/allinea_performance_reports/_index.md
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diff --git a/content/guides/running_applications/allinea_profiling_and_debugging/allinea_performance_reports/blast_with_allinea_performance_reports.md b/content/Applications/Application_Specific_Guides/allinea_profiling_and_debugging/allinea_performance_reports/blast_with_allinea_performance_reports.md
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rename from content/guides/running_applications/allinea_profiling_and_debugging/allinea_performance_reports/blast_with_allinea_performance_reports.md
rename to content/Applications/Application_Specific_Guides/allinea_profiling_and_debugging/allinea_performance_reports/blast_with_allinea_performance_reports.md
diff --git a/content/guides/running_applications/allinea_profiling_and_debugging/allinea_performance_reports/lammps_with_allinea_performance_reports.md b/content/Applications/Application_Specific_Guides/allinea_profiling_and_debugging/allinea_performance_reports/lammps_with_allinea_performance_reports.md
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diff --git a/content/guides/running_applications/allinea_profiling_and_debugging/allinea_performance_reports/ray_with_allinea_performance_reports.md b/content/Applications/Application_Specific_Guides/allinea_profiling_and_debugging/allinea_performance_reports/ray_with_allinea_performance_reports.md
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rename from content/guides/running_applications/allinea_profiling_and_debugging/allinea_performance_reports/ray_with_allinea_performance_reports.md
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diff --git a/content/guides/running_applications/allinea_profiling_and_debugging/using_allinea_forge_via_reverse_connect.md b/content/Applications/Application_Specific_Guides/allinea_profiling_and_debugging/using_allinea_forge_via_reverse_connect.md
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diff --git a/content/guides/running_applications/bioinformatics_tools/_index.md b/content/Applications/Application_Specific_Guides/bioinformatics_tools/_index.md
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diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/_index.md b/content/Applications/Application_Specific_Guides/bioinformatics_tools/alignment_tools/_index.md
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diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/_index.md b/content/Applications/Application_Specific_Guides/bioinformatics_tools/alignment_tools/blast/_index.md
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rename from content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/_index.md
rename to content/Applications/Application_Specific_Guides/bioinformatics_tools/alignment_tools/blast/_index.md
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/create_local_blast_database.md b/content/Applications/Application_Specific_Guides/bioinformatics_tools/alignment_tools/blast/create_local_blast_database.md
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rename from content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/create_local_blast_database.md
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diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md b/content/Applications/Application_Specific_Guides/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md
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rename from content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md
rename to content/Applications/Application_Specific_Guides/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blat.md b/content/Applications/Application_Specific_Guides/bioinformatics_tools/alignment_tools/blat.md
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rename from content/guides/running_applications/bioinformatics_tools/alignment_tools/blat.md
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diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/bowtie.md b/content/Applications/Application_Specific_Guides/bioinformatics_tools/alignment_tools/bowtie.md
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rename from content/guides/running_applications/bioinformatics_tools/alignment_tools/bowtie.md
rename to content/Applications/Application_Specific_Guides/bioinformatics_tools/alignment_tools/bowtie.md
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/bowtie2.md b/content/Applications/Application_Specific_Guides/bioinformatics_tools/alignment_tools/bowtie2.md
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diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/_index.md b/content/Applications/Application_Specific_Guides/bioinformatics_tools/alignment_tools/bwa/_index.md
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diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/running_bwa_commands.md b/content/Applications/Application_Specific_Guides/bioinformatics_tools/alignment_tools/bwa/running_bwa_commands.md
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diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/clustal_omega.md b/content/Applications/Application_Specific_Guides/bioinformatics_tools/alignment_tools/clustal_omega.md
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rename from content/guides/running_applications/bioinformatics_tools/alignment_tools/clustal_omega.md
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diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/tophat_tophat2.md b/content/Applications/Application_Specific_Guides/bioinformatics_tools/alignment_tools/tophat_tophat2.md
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diff --git a/content/guides/running_applications/bioinformatics_tools/biodata_module.md b/content/Applications/Application_Specific_Guides/bioinformatics_tools/biodata_module.md
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diff --git a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/_index.md b/content/Applications/Application_Specific_Guides/bioinformatics_tools/data_manipulation_tools/_index.md
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diff --git a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/bamtools/_index.md b/content/Applications/Application_Specific_Guides/bioinformatics_tools/data_manipulation_tools/bamtools/_index.md
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diff --git a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/bamtools/running_bamtools_commands.md b/content/Applications/Application_Specific_Guides/bioinformatics_tools/data_manipulation_tools/bamtools/running_bamtools_commands.md
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diff --git a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/_index.md b/content/Applications/Application_Specific_Guides/bioinformatics_tools/data_manipulation_tools/samtools/_index.md
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diff --git a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/running_samtools_commands.md b/content/Applications/Application_Specific_Guides/bioinformatics_tools/data_manipulation_tools/samtools/running_samtools_commands.md
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diff --git a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/sratoolkit.md b/content/Applications/Application_Specific_Guides/bioinformatics_tools/data_manipulation_tools/sratoolkit.md
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diff --git a/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/_index.md b/content/Applications/Application_Specific_Guides/bioinformatics_tools/de_novo_assembly_tools/_index.md
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diff --git a/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/oases.md b/content/Applications/Application_Specific_Guides/bioinformatics_tools/de_novo_assembly_tools/oases.md
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diff --git a/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/ray.md b/content/Applications/Application_Specific_Guides/bioinformatics_tools/de_novo_assembly_tools/ray.md
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diff --git a/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/soapdenovo2.md b/content/Applications/Application_Specific_Guides/bioinformatics_tools/de_novo_assembly_tools/soapdenovo2.md
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--- /dev/null
+++ b/content/Applications/_index.md
@@ -0,0 +1,9 @@
++++
+title = "Guides"
+weight = "20"
++++
+
+In-depth guides to using HCC resources
+--------------------------------------
+
+{{% children description="true" %}}
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-+++
-title = "Running Applications"
-description = "How to run various applications on HCC resources."
-weight = "20"
-+++
-
-{{% children %}}
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-+++
-title = "Compiling Source Code"
-description = "How to compile source code of various types on HCC resources."
-+++
-
-Compiling source code on HCC machines is done with compiler environments
-configured by the `module` utility. The utility adds directives to the
-environment and adds executables to the `PATH` so that users and jobs
-can directly call the compilers.
-
-### Finding available compiler Modules
-
-{{< highlight bash >}}
-$ module spider compiler
-{{< /highlight >}}
-
-This command will list available compiler modules to load.
-
-### Loading Modules
-
-{{< highlight bash >}}
-$ module load <module>
-{{< /highlight >}}
-
-This command will load an available module. The modules are usually in
-the form of `compiler/<name>/<version>`.
--
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