I've read about embedding text files (or any other resource for that matter) into binaries, and I'm doing it like so:
objcopy -I binary -O elf32-littlearm --binary-architecture arm myfile.txt myfile.txt.o
However, unlike in the tutorial, I get the following response:
ld: unknown architecture of input file `myfile.txt' is incompatible with arm output
The example uses i386 but this doesn't seem to be the issue either as I can't do it that way either.
Is there a way I can force objcopy to ignore the fact it's a text file and not a valid compatible binary so it just copies it byte-for-byte into my program?
For data only object file (no code), you can skip binary-architecture option.
So the following should work
objcopy -I binary -O elf32-littlearm myfile.txt myfile.txt.o to generate object file.
Related
I am very new to coding so I'm not really sure how to approach this. I wanted to look at some data that we got and sequence them using Bismark. I already used Trim Galore to pare the reads, now I wanted to get the data into Bismark. However, I'm not exactly sure how to approach this. In the documentation it said that it required Perl to run so I downloaded Perl along with the Bismark zip file from github. I also downloaded the bowtie2 zip file and extracted both the zip files into the same directory. I then opened up the Perl command prompt and set the directory to one with my extracted folders.
I put this line in:
> \bismark\bismark_genome_preparation --path_to_bowtie ^
C:\Users\sevro\Documents\Lab_Code\bowtie2-master --verbose ^
C:\Users\sevro\Documents\Lab_Code\genome
The system cannot find the path specified.
I also tried this after changing the directory to the Bismark folder:
> perl bismark
Failed to execute Bowtie 2 porperly (return code of 'bowtie2 --version' was 256).
Please install Bowtie 2 or HISAT2 first and make sure it is in the PATH,
or specify the path to the Bowtie 2 with --path_to_bowtie2 /path/to/bowtie2,
or --path_to_hisat2 /path/to/hisat2
I tried a few other things but all in all I am a bit confused on how exactly to approach this. Things I have downloaded right now:
Bismark zip file- https://github.com/FelixKrueger/Bismark
Bowtie2 zip file- https://github.com/BenLangmead/bowtie2
A genome assembly in .fa format
The data that I want to analyze in fasta format
Any insight would be helpful.
I think Bismark and bowtie2 only supports Linux and macOS natively. If you want to use bismark on Windows you can try install it via a *nix emulation systems like Cygwin, MSYS2, or simply use WSL. I tested this on Windows 11 with WSL with Ubuntu 20.04:
Downloaded bowtie2-2.4.4-linux-x86_64.zip and extracted to ~/bowtie2/bowtie2-2.4.4-linux-x86_64 folder.
Downloaded Bismark-0.23.1.zip and extracted to ~/bismark/Bismark-0.23.1/
Tested installation:
$ perl --version
This is perl 5, version 30, subversion 0 (v5.30.0) built for x86_64-linux-gnu-thread-multi (with 50 registered patches, see perl -V for more detail)
$ perl bismark --path_to_bowtie2 ../../bowtie2/bowtie2-2.4.4-linux-x86_64/Bowtie 2 seems to be working fine (tested command '../../bowtie2/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4])
Output format is BAM (default)
Did not find Samtools on the system. Alignments will be compressed with GZIP instead (.sam.gz)
Genome folder was not specified!
DESCRIPTION
The following is a brief description of command line options and arguments to control the Bismark
bisulfite mapper and methylation caller. Bismark takes in FastA or FastQ files and aligns the
reads to a specified bisulfite genome. Sequence reads are transformed into a bisulfite converted forward strand
version (C->T conversion) or into a bisulfite treated reverse strand (G->A conversion of the forward strand).
Each of these reads are then aligned to bisulfite treated forward strand index of a reference genome
(C->T converted) and a bisulfite treated reverse strand index of the genome (G->A conversion of the
forward strand, by doing this alignments will produce the same positions). These 4 instances of Bowtie 2 or HISAT2
are run in parallel. The sequence file(s) are then read in again sequence by sequence to pull out the original
sequence from the genome and determine if there were any protected C's present or not.
The final output of Bismark is in BAM/SAM format by default, described in more detail below.
USAGE: bismark [options] <genome_folder> {-1 <mates1> -2 <mates2> | <singles>}
[...]
I have STM32F404 board and I am trying to flash it. I am following this tutorial.
In the project Makefile
$(PROJ_NAME).elf: $(SRCS)
$(CC) $(CFLAGS) $^ -o $#
$(OBJCOPY) -O ihex $(PROJ_NAME).elf $(PROJ_NAME).hex
$(OBJCOPY) -O binary $(PROJ_NAME).elf $(PROJ_NAME).bin
burn: proj
$(STLINK)/st-flash write $(PROJ_NAME).bin 0x8000000
The bin file is generated using OBJCOPYand then flashed using the Make target burn
My questions :
Question 1: What does OBJCOPY=arm-none-eabi-objcopy in this case. I opened the man but I didn't fully undrestand can anyone explain it simply ?
Question 2: Flashing the bin file gives the expected result (Leds blinking) However the leds are not blinking by flashing the elf file $(STLINK)/st-flash write $(PROJ_NAME).elf 0x8000000 so why ?
Question 1: What does OBJCOPY=arm-none-eabi-objcopy in this case. I opened the man but I didn't fully undrestand can anyone explain it simply ?
It assigns value arm-none-eabi-objcopy to make variable OBJCOPY.
When make executes this command:
$(OBJCOPY) -O binary $(PROJ_NAME).elf $(PROJ_NAME).bin
the actual command that runs is
arm-none-eabi-objcopy -O binary tim_time_base.elf tim_time_base.bin
Question 2: Flashing the bin file gives the expected result (Leds blinking) However the leds are not blinking by flashing the elf file $(STLINK)/st-flash write $(PROJ_NAME).elf 0x8000000 so why?
The tim_time_base.elf is an ELF file -- it has metadata associated with it. Run arm-none-eabi-readelf -h tim_time_base.elf to see what some of this metadata are.
But when you processor jumps to location 0x8000000 after reset, it is expecting to find executable instructions, not metadata. When it finds "garbage" it doesn't understand, it probably just halts. It certainly doesn't find instructions to blink the lights.
In case someone wants to use the DFU ("Do a Firmware Upgrade") function, this tutorial teaches how to use the binary file to be loaded via USB, when the STM32 is operating with USB Host (or maybe OTG):
STM32 USB training - 11.3 USB MSC DFU host labs
This tutorial is part of a series of videos that are highly recommended for the programmer to watch, to understand a little better how the STM32 USB ports work and use (videos provided by the STM32 manufacturer itself, I recommend that the programmer watch all the videos on this channel):
MOOC - STM32 USB training
Notes: The example code from the STM32 tutorials are available in the descriptions of the videos themselves.
The binary file (*.bin) can be obtained with the help of the command that the colleague above explained (Employed Russian), and it (command) can also be adapted to produce a file containing the comparison value for CRC usage, as can be seen some details in these following posts:
Hands-on: CRC Checksum Generation
Srec_cat could be used to generate CRC checksum and put it into HEX
file. To simplify the process, please put srec_cat.exe into the root
of project folder.
Some tips and solutions about this CRC usage (Windows/Linux)
Unfortunately the amount of code is too big to post here directly, but I leave the code related to the other answer below:
arm-none-eabi-objcopy -O ihex "${BuildArtifactFileBaseName}.elf"
"${BuildArtifactFileBaseName}.hex" && ..\checksum.bat
${BuildArtifactFileBaseName}.hex
Contents of the checksum.bat file:
#!/bin/bash
# Windows [Dos comment: REM]:
#..\srec_cat.exe %1 -Intel -fill 0xFF 0x08000000 0x080FFFFC -STM32 0x080FFFFC -o ROM.hex -Intel
# Linux [Linux comment: #]:
srec_cat $1 -Intel -fill 0xFF 0x08000000 0x080FFFFC -STM32 0x080FFFFC -o ROM.hex -Intel
Note: In this case, the file to be written is ROM.hex (you will need to configure the STM32CubeIDE to be able to do this operation, the IDE uses the *.elf file, see how to do it in the tips above)
This other tutorial deals with using the file with *.DFU extension:
DFU - DfuSe
The key benefits of the DFU Boatloader are: No specific tools such us
JTAG, ST-LINK or USB-to-UART cable are needed. The ability to program
an "empty" STM32 device in a newly-assembled board via USB. And easy
upgrade the STM32 firmware during development or pre-production.
This need to use a HEX file facilitates the operation of the implementation of the ROM.hex file generated with the CRC value, being practically a continuity:
You must generate a .DFU file from an .HEX or .S19 file, for do this
use the DFU File Manager.
But it seems that using the *.DFU file is not as standalone as using the *.BIN file, so I found this other code that converts the HEX file (generated with CRC) to the *.BIN file, which can be used with a USB stick, as per the tutorial cited at the beginning of this answer (11.3 USB MSC DFU host):
objcopy --input-target=ihex --output-target=binary code00.hex code00.bin
Source
It sounds a little confusing, but we have these steps:
1- The STM32CubeIDE generates the *.elf file.
2- After compilation, the *.elf file is converted to *.hex.
3- CRC value is added in *.hex file via srec_cat application.
4- Now the *.hex file is converted to *.bin.
5- The BIN file is then stored on a USB flash drive.
6- STM32 updates firmware using USB flash drive file.
To use the *.BIN file it is necessary that the STM32 is already programmed to load the BIN file. If it is not programmed (the STM32 is empty, virgin or the program was not made to load the BIN file), it will be necessary to use St-Link or another programmer, or perhaps making use of the DFU method described in the tutorial above (DFU - DfuSe).
I am using PDFtk (Version 2.02, UNIX) for merging PDF and facing below problems in the output PDF:
Initial View of the PDF is changed (should open with Bookmarks Panel and Page)
Bookmarks doesn’t point to the exact linked section as in the separate PDFs (shows fit page of the section)
Original metadata is lost (should retain first PDF's metadata)
Please suggest any workaround for the above points.
Regards,
Umesh
It's a little late to answer, but I came across this question while looking for a solution to the same problem. After taking a look at the man of pdftk I found a solution and I made a little script:
#!/usr/bin/env bash
# pdfcat
array=( $# )
len=${#array[#]}
merged=${array[$len-1]}
pdf2merge=${array[#]:0:$len-1}
pdftk $1 dump_data output metadata
pdftk $pdf2merge cat output $merged
pdftk $merged update_info metadata output out
mv out $merged
rm metadata
exiftool $merged
The script save the metadata of the first PDF file (first argument) and write it to a file called metadata. Then it uses the cat command of pdftk to merge all the files (the output file is the last argument). Finally it loads metadata's content to the metadata of the resulting file before erasing metadata. The last line uses exiftoolto print the metadata of the resulting file in order to check if everything went well.
You can save this script to your home/username/bin directory, make it executable with:
$ chmod u+x scriptname
and then you can use it to merge files with the following syntax:
$ scriptname 1.pdf 2.pdf 3.pdf output.pdf
The resulting output.pdf will have the same metadata as the original 1.pdf file.
I have tried using ld to link 2 .o files together with this,
ld -T link.ld -o kernel.bin kernel.o ks.o
but it produce an error saying
ld: cannot open linker script file link.ld: No such file or directory
Is there anything wrong with my commands or do i have to create a path or something?
You need to create the "linker script" link.ld. Google "linker script" for docs.
Is it possible to remove a file using a build phase in xcode 4 based on if it is release or dev?
If so has anyone got an example?
I have tried :
if [ "${CONFIGURATION}" = "Debug" ]; then
find "$TARGET_BUILD_DIR" -name '*-live.*' -print0 | xargs -0 rm
fi
This prints CopyStringsFile
"build/Debug-iphonesimulator/Blue Sky.app/PortalText-live.strings" CDL/PortalText-live.strings
cd "/Users/internet/Desktop/iPhone Template/iPhonePortalTemplate/CDL.Labs"
setenv PATH "/Developer/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/usr/bin:/Developer/Applications/Xcode.app/Contents/Developer/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin"
builtin-copyStrings --validate --inputencoding utf-8 --outputencoding binary --outdir "/Users/internet/Desktop/iPhone Template/iPhonePortalTemplate/CDL.Labs/build/Debug-iphonesimulator/Blue Sky.app" -- CDL/PortalText-live.strings
But does actually remove the file from the bundle.
The only way I've ever had different files, is having a separate Target, and only include certain files in certain targets.
EDIT WITH AN EXAMPLE
Ok, I've done exactly the same in another project. We had a DefaultProperties.plist file, which was included in the target.
We then had 3 copies of this, NOT included in the target, ProdProperties.plist, TestProperties.plist, UatProperties.plist.
We built for environments on the command line, using xcodebuild, as it was built using an automated build server (Bamboo).
Prior to executing xcodebuild, we would run this:
cp -vf "./Properties/Environments/${environment}Properties.plist" ./Properties/shared/DefaultProperties.plist
touch Properties/shared/DefaultProperties.plist
with $(environment) being passed into the script.
You could do something like this with the RunScript phase in Xcode.