added test_data/README.md

gpertea · gpertea · commit 1bf55ed6ef6b · 2019-07-30T15:28:20.000-04:00
diff --git a/README.md b/README.md
@@ -1,14 +1,17 @@
 ## Obtaining and installing StringTie
 
 Source and binary packages for this software, along with a small test data set 
-can be directly downloaded from the <a href="https://github.com/mpertea/stringtie2/releases">Releases</a> page for this repository. StringTie is compatible with a wide range of Linux and Apple OS systems (going as far back as RedHat Enterprise Linux 5.0 and OS X 10.7). The main program (StringTie) does not have any other library dependencies and in order to compile it from source it requires only a C++ compiler which supports the C++ 0x standard (GCC 4.5 or newer).
+can be directly downloaded from the <a href="https://github.com/gpertea/stringtie/releases">Releases</a> page for this repository. 
+StringTie is compatible with a wide range of Linux and Apple OS systems (going as far back as RedHat Enterprise Linux 5.0 and OS X 10.7). 
+The main program (StringTie) does not have any other library dependencies and in order to compile it from source it requires only 
+a C++ compiler which supports the C++ 0x standard (GCC 4.5 or newer).
 
 ### Building the latest version from the repository 
 In order to compile the StringTie source in this GitHub repository the following steps can be taken:
  
 ```
-git clone https://github.com/mpertea/stringtie2
-cd stringtie2
+git clone https://github.com/gpertea/stringtie
+cd stringtie
 make release
 ```
 
@@ -27,7 +30,7 @@ Instead of compiling from source, some users may prefer to download an already c
 and Apple OS X, ready to run. These binary package releases are compiled on older versions of these 
 operating systems (RedHat Enterprise Linux 5.0 and OS X 10.7) in order to provide compatibility with 
 a wide range of (older) OS versions, not just the most recent versions. These precompiled packages are 
-made available on the <a href="https://github.com/mpertea/stringtie2/releases">Releases</a> page for this repository.
+made available on the <a href="https://github.com/gpertea/stringtie/releases">Releases</a> page for this repository.
 Please note that these binary packages do not include the optional [super-reads module](#the-super-reads-module), 
 which currently can only be built on Linux machines, from the source made available in this repository.
 
@@ -60,7 +63,9 @@ cd stringtie-2.0.Linux_x86_64
 ./run_tests.sh
 ```
 
-These small test/demo data sets can also be downloaded separately as <a href="https://github.com/mpertea/stringtie2/releases/download/v2.0/test_data.tar.gz">test_data.tar.gz</a> along with the source package and pre-compiled packages on the <a href="https://github.com/mpertea/stringtie2/releases">Releases</a> page for this repository.
+These small test/demo data sets can also be downloaded separately as <a href="https://github.com/gpertea/stringtie/releases/download/v2.0/test_data.tar.gz">test_data.tar.gz</a> 
+along with the source package and pre-compiled packages on the <a href="https://github.com/gpertea/stringtie/releases">Releases</a> 
+page of this repository.
 
 The tests can also be run manually as shown below (after changing to the _test_data_ directory, `cd test_data`):
 
@@ -85,7 +90,7 @@ stringtie -L -G human-chr19_P.gff -o long_reads_guided.out.gtf long_reads.bam
 ```
 
 The above runs should take around one second each on a regular Linux or MacOS desktop. 
-(see also <a href="https://github.com/mpertea/stringtie2/blob/master/test_data/README.md">test_data/README.md</a>).
+(see also <a href="https://github.com/gpertea/stringtie/blob/master/test_data/README.md">test_data/README.md</a>).
 
 For very large data sets one can expect up to one hour of processing time. A minimum of 8GB of RAM is recommended for running StringTie on regular size RNA-Seq samples, with 16 GB or more being strongly advised for larger data sets.
 
@@ -186,7 +191,7 @@ This optional module can be used to de-novo assemble, align and pre-process
 RNA-Seq reads, preparing them to be used as "super-reads" by Stringtie.
 
 Mode detailed information is provided in the 
-<a href="https://github.com/mpertea/stringtie2/blob/master/SuperReads_RNA/README.md">SuperReads_RNA/README.md</a>.
+<a href="https://github.com/gpertea/stringtie/blob/master/SuperReads_RNA/README.md">SuperReads_RNA/README.md</a>.
 Quick installation instructions for this module from the source available on this repository 
 (assuming the above Stringtie installation was completed):
 
@@ -197,7 +202,7 @@ Quick installation instructions for this module from the source available on thi
 
 ### Using super-reads with Stringtie
 
-After running the super-reads module (see the <a href="https://github.com/mpertea/stringtie2/blob/master/SuperReads_RNA/README.md">SuperReads_RNA</a> module documentation for usage details), there 
+After running the super-reads module (see the <a href="https://github.com/gpertea/stringtie/blob/master/SuperReads_RNA/README.md">SuperReads_RNA</a> module documentation for usage details), there 
 is a BAM file which contains sorted alignment for both short reads and super-reads, called *`sr_merge.bam`*, 
 created in the selected output directory. This file can be directly given as the main input file
 to StringTie as described in the [Running StringTie](#running-stringtie) section above.
diff --git a/run_tests.sh b/run_tests.sh
@@ -22,7 +22,7 @@ if [ ! -f test_data/human-chr19_P.gff ]; then
   else
     echo "..Downloading test data.."
     #use curl to fetch the tarball from a specific github release or branch
-    curl -sLJO https://github.com/mpertea/stringtie2/raw/test_data/test_data.tar.gz
+    curl -sLJO https://github.com/gpertea/stringtie/releases/download/v2.0/test_data.tar.gz
     unpack_test_data
   fi
 fi
diff --git a/test_data/README.md b/test_data/README.md
@@ -0,0 +1,40 @@
+## Test data
+
+The test data can be automatically retrieved by the `run_tests.sh` script included 
+with all source or binary distributions of StringTie, or downloaded separately from this url:
+https://github.com/gpertea/stringtie/raw/test_data/test_data.tar.gz
+
+The `run_tests.sh` script will then run StringTie on these data sets and compare the output with the 
+precomputed, expected output for each case. If the output of each test matches the 
+expected output, the test is considered successful (and "OK." will be shown on the next line), 
+otherwise an error will be reported.
+
+## Running StringTie on the test data separately
+
+The command lines shown below assume that the _stringtie_ program is installed somewhere 
+in the shell's PATH. If that is not the case, the `stringtie` comand below should be prepended 
+with the directory path to the _stringtie_ executable
+
+### Test 1: Input consists of only alignments of short reads
+
+```
+stringtie -o short_reads.out.gtf short_reads.bam
+```
+
+### Test 2: Input consists of alignments of short reads and superreads
+
+```
+stringtie -o short_reads_and_superreads.out.gtf short_reads_and_superreads.bam
+```
+    
+### Test 3: Input consists of alignments of long reads
+
+```
+stringtie -L -o long_reads.out.gtf long_reads.bam
+```
+    
+### Test 4: Input consists of alignments of long reads and reference annotation (guides)
+
+```
+stringtie -L -G human-chr19_P.gff -o long_reads_guided.out.gtf long_reads.bam
+```
